The Cranfield Genome Browser - CRAMER

Introduction

CRAMER is a customisable, JavaScript and Jade based genome browser for interactive exploration of genomic data. Data is visualized in the browser, meaning CRAMER can be installed on any website and show data from a wide range of online, ftp links or local sources. CRAMER works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3, BAM or delimited text files, and can be customised to parse and display any data source as required.

The application and source code is freely available to download from the CRAMER Github repository: https://github.com/FadyMohareb/cramer.

Although it is possible to get the docker image to work on Mac, the process can be tricky and not very stable. This is mainly due to the fact that the host networking driver currently only works on Linux hosts (See more information here: https://docs.docker.com/network/network-tutorial-host/). It's possible to use a different port for the application, however access to the "helper" tools such as tabix and samtools can be tricky. Therefore, we do recommend the manual installation on Mac, and this is quite straight forward as shown below:

Option 2: Manual installation

First of all, make sure you have all the Dependencies installed. Make sure that they are available on the $PATH. (Typically installed under /usr/local/bin). To check whether this is the case, type

echo $PATH

This should include (among other paths) usr/local/bin.

Clone the Github repository with the following command:

git clone https://github.com/FadyMohareb/cramer

To install, run the following commands:

cd \<cramer/Directory\>

npm install

node bin/www

The output should be:

Running at port: \<port\>

MongoDB connection open

Then, it could be accessible from any browser on any operating systems. Open your browser and write this in the URL address. Make sure the port value is the same than in the output displayed in the prompt command:

localhost:\<port\>

OR

IPaddress:\<port\>

To begin adding visualisation instances, you need to add a new admin user using the following command:

npm run newUser <user@example.com> <password> <John>

For example: npm run newUser admin@admin.com adminadmin admin

Once installed, the multiple files that form the program can be altered to change the functionalities of the program as the developer team wants, and then saved to apply these changes. However, modified files which are contained in list-js.js would require building the program before running it to apply the changes. This can be done with the following command:

$ npm run-script build

CRAMER workflow

CRAMER consists of multiple web pages backed by a node server, and a mongo database. It provides a number of web pages to assist with setting up and visualising genomic tracks (Fig. 1), with the actual genome browser page as the main gateway for the program. It is made up of a set of tracks – horizontal sections of the browser which display features, such as genes or variants, – which share the same start and end position. These features can either be fetched from Ensembl or extracted from a local or FTP file. Currently, the browser supports the following types of data files: FASTA, BED, BIGBED, BAM, WIG, BIGWIG, GFF, GFF3, GTF, VCF and RSEM genes.results. In addition, CRAMER has a series of plugins which add extra functionalities.

The plugins and tracks can be configured on the instance webpage. An instance is a combination of a chosen genome, a choice of the plugins to implement, and a selection of the tracks to visualize; that will be displayed in the browser. The genome data could be obtained from a local file or through Ensembl database.

$C:\Users\Sergio\Desktop\forsergio.png$

Fig.1. Diagram of the relation between the multiple webpages that form CRAMER

The welcome webpage allows registered users to create new instances or view and modify already existing instances. Non-registered users are still able to view and explore existing instances however they do not have the right to create or modify instances. Our intention is not to provide the system users with means to register and add their own instances; instead, this functionality is reserved to the genome browser administrator (or group of administrators) to manage, on behalf of the research group. The reasoning behind this is to control the size of the database and storage space on the deployment server, by preventing the users uploading duplicating genome files and/or large bam files which may result in running out of disk space quite quickly with genomic data. Since all the webpages are connected to an external server and a database, the data that is introduced from any device is stored in the database and is readily accessible from any other device.

File requisites

The numerous file types that the genome browser can support must adhere to certain formatting rules. Any of the changes that are required to convert the files into compatible files are to be carried out by the user prior to loading them into the web application. The requirements for compatibility for each file type are the following:

GFF, VCF, and BED: These files must be gzipped and indexed using tabix with the index file in the same directory [1]. The program will be able to automatically distinguish the characteristic chromosome IDs from the full chromosome names of the file, as long as the IDs are at the end of the name (for example SL2.50ch01).
FASTA: These files must be indexed using faidx with the index file in the same directory [2], and the chromosome names have to be formatted as chr[num] (for example chr1).
RSEM genes.results: Matching gene IDs should be included in the GFF file that is loaded with this file format as the genomic coordinates of the genes will be fetched from it.
Genomic BAM: These files must be gzipped and indexed with SAMtools with the index file in the same directory [2]. Like with tabix indexed files, the program will be able to automatically distinguish the characteristic chromosome IDs from the full chromosome names of the file, as long as the IDs are at the end of the name (for example SL2.50ch01). This can be pre-processed using the "processingBAM.sh" script.
read coverage BIGWIG: These files can be made compatible with CRAMER by using the "processingBAM.sh" script that is included with the program. This script automates the steps to configure the BAM file and generate a BIGWIG file for FTP loading, which can be loaded into the program.

The script can be executed by typing ./processingBAM.sh input.bam in a Linux terminal, and following the instructions that will be prompted on the screen.

Beware that for using the script and loading the file via FTP correctly the chromosome IDs must be at the end of the chromosome name (for example SL2.50ch01) as indicated for previous files. The script requires the following tools to be fully executed: samtools, bam2wig, and ucsc-wigtobigwig (installed through bioconda) [3]. Any BIGWIG that follows this format can be used.

In addition to this, local files can be dragged and dropped in the genome browser window. The drag-and-drop action is available for the following types of files, with the prerequisite that their indexed file is also stored in the same location: GFF, GFF3, GTF, VCF, BED, BIGBED, WIG, BIGWIG and BAM files can all be dragged and dropped into the user interface but their format is restricted to chromosome numbers formatted as chr[num] or [num] (for example chr01 or 1).

How to create a new user account

The administrator can create new user accounts via the command line by typing the following:

npm run newUser <user@example.com> <password> <John>

The required inputs are the user's email address, the password and a user name.

Sign in

Registered users can sign in by clicking on the sign in link on the home page and entering their login credentials on the login page (Fig. 2).

Fig.2. Login page for registered users.

Tracks

Currently, CRAMER has sixteen different tracks available that can be divided into three groups: Standard tracks, Ensembl tracks, and File tracks.

There are two Standard tracks which can work without the need to fetch data from Ensembl or upload a file:

Scalebar: Displays a bar which provides information regarding the current position in the chromosome.
Chromosome: Displays the karyotype of the selected chromosome.

The Ensembl tracks are only available when the user chooses a genome from the Ensembl database. There are three Ensembl tracks:

Ensembl Genes: Fetches data from Ensembl and displays the genes that are present in the chosen chromosome positions. It also displays a legend for each gene.
Ensembl Sequence: Fetches data from Ensembl and displays the nucleotide sequence of the chromosome. Each base has a different colour assigned. Adenine (A) is green, Thymine (T) is red, Cytosine (C) is blue, and Guanine (G) is yellow.
SNP Database: Fetches data from Ensembl and displays the single nucleotide polymorphisms (SNPs) present for the selected positions of the chromosome. It also displays a legend.

The File tracks work in a different way to the others. A user can generate multiple tracks of each type with a name, a short description, and an URL or file path to the file that the user wants to display on the browser. Each track type has different configurable properties, such as the threshold for example, due to the nature of the file. Each track type can be individually activated, deactivated and any tracks created can be removed. There are eight File tracks available:

FASTA sequence: Displays the chromosome sequence from a FASTA file.
BED Annotation: Displays the positions and details of annotation from a BED file.
Genomic BAM Transcripts: Displays the sequences of reads from a genomic BAM.
BIGWIG Graph: Displays the contents of a BIGWIG file as a graph.
GFF Genes: Displays a GFF file with all the components forming a gene with exons and introns represented.
VCF Variants: Displays the position of each variation and whether they are higher or lower than the quality threshold set. Requires a VCF file.
SNP Density Graphs: Displays the density of SNPs over a range of positions. Requires a VCF file.
Gene Expression Graphs: Displays the predicted counts at the position of each gene.

Finally, there is an additional track available within the File tracks, called Custom track. A Custom track must be written as a JavaScript object, which will be implemented into the program. There is no limit to the number of Custom tracks a user can create.

Plugins

Table 1. provides a summary and short description of the plugins available in CRAMER.

Table 1. Plugins included in CRAMER.

Plugin	Implements:
Karyotype	An ideogram of the selected chromosome on the top of the browser. A marker on the ideogram that reports the current position in the chromosome. This marker can be dragged and resized, which will update the positions of the tracks to match the positions of the markers.
Track Controls	An additional menu in each track which provides the option to display info about the track, or to delete it.
Resizer	A handler at the bottom of each track that can be vertically dragged to resize the track.
Focus Region	A button on the control panel that resets the start and end positions currently displayed to the default ones of the instance.
Tooltips	A button that displays a brief description of each element in the genome browser.
Select Chromosome	A button that displays a list of all the chromosomes for the visualised genome. A chromosome can be displayed by clicking on the chromosome number on the list.
Search	A button that displays a pop-up window which provides the option to search by gene name, gene position, gene name AND position, or ENSEMBL id in the currently displayed chromosome.
File Drop	Allows users to drag and drop a file -in a format supported by CRAMER - directly into the browser and display it.

How to navigate CRAMER

Welcome page

$C:\UNIVERSIDAD\Applied Bioinformatics\Group Project\STARTING DEF\User Guide\Screenshots\Screenshot_Welcome_page.png$

Fig.3. Welcome page of the program for a logged-in user.

The welcome page is where users can access existing instances. Registered users can also log-in which provides them with the option to create, modify or remove instances (Fig. 3).

On the top of the page, there is a brief welcome message and description of what the user can do (A). Next to it, on the right side, depending on whether the user is registered or not there can be different buttons (B):

Sign in: Registered users can sign in to unlock additional actions; this will direct them to the login webpage.
Create a new instance and Sign out: Logged-in users can create new instances, which will redirect them to the instances webpage, or sign out of their accounts.

A list of all the available instances is displayed in the centre of the welcome (C). The names of the instances are highlighted in blue (D), followed by a brief description of each instance in black (E). The name of the instances (D) are also links to the instance deployment on the genome browser itself. If the user is logged-in there will be two additional buttons:

Modify: A registered user can modify instances that are already created (F). This button will redirect the user to the instances webpage.
Remove: A registered user can delete an instance that is already created (G). Clicking on the button will make a pop-out window asking confirmation appear, if the user clicks on “OK”, the instance will be deleted.

Instance page

Fig.4. (A) Instance page with examples of how to fill each field. (B) Pop-up window to create a new sub-track in the GFF Gene parent track.

The instance page is accessed through the “Create new instance” or “Modify” button on the welcome page (Fig. 4A). This page is only available for registered users and allows creating or modifying an instance. When a new instance is being created, all the fields will be empty. In contrast, if an instance is being modified all the previous configurations will be provided in each field.

In the fields marked “Project Name” (A) and “Description” (B) the user can insert the instance name and a short description which will be displayed in the welcome page. Other fields required to be filled include: “Genome” (C), for the species genome, “Chromosome” (D) for the chromosome number in which the instance will be initialized (D), “Start” (E) and “End” (F) which need to be filled with the start and end positions of the chromosome to be displayed. The species genome karyotype (C) can be fetched from the Ensembl database, uploaded from a local file or selected from a list of already available genomes. These options can be switched by a button next to the genomes (G), which is formed by three sub-buttons, one per each option. The uploaded file needs to follow the format described in the Appendix.

On the right top corner of the screen, there is also a “Home” button (H) which redirects the user to the welcome page.

Other features of the instance page include a list with the available plugins for the current instance (I), and a checkbox to activate/deactivate individual plugins (K, L).

In the case where an Ensembl species genome has been selected, an additional panel will appear underneath the “Plugins” entitled “Ensembl tracks” (M). The functionality of this type of tracks has been described in the Tracks section above.

The other two types of tracks Standard and File, are grouped together in the “‘Tracks” box (N) adjacent to the “Plugins” box. The file tracks are highlighted in blue (O) and next to them there is a blue plus-shape button (P). Clicking on this button will display a pop-up window which allows creating a track by filling all the required forms (Fig. 4B). Once a track is created, clicking on the track type (O) will reveal all the tracks of this type (Q). A track can be deleted by clicking on the remove button (R). In the case where the user wishes to display data from a local file on a track, a track with an FTP file link needs to be created. It is the responsibility of the user to write the FTP link to the correctly formatted file in order to get a correct track display. In addition, a custom track can be created by selecting the “Custom Track” option at the bottom of this list (S).

Finally, an instance can be saved in the database by clicking on the “Submit” button (T). If any parameters are incomplete or wrongly filled, a red alert will inform the user about the cause of the error.

Genome browser page

Fig.5. Genome browser page. In the browse is displayed the karyotype of the chromosome 5 of Mus musculus and the genes found in Ensembl for the current view position.

The genome browser page (Fig. 5) is where all the data of the instances is visually represented. The interface consists of a set of tracks, each representing a different type of data. On the left side of the browser window there is a vertical panel with labels for each track (A) and a small handler which allows the user to vertically drag the track and relocate it (B). On the right side of the browser window, there is a small menu tab (C) which allows the user to get more info about the current track, adjust the height or remove the track altogether.

On the top corner of the left panel, there is a “Tracks” button (D) which displays a pop-out window where all the current implemented tracks are listed. From there, any implemented track can be removed (clicking on the “x” shape button) or added (clicking on the “+” shape button), even if it has already been added.

The karyotype of the chromosome is displayed on a ribbon located at the top of the browser window (E). Users can navigate through the chromosome by clicking and dragging on the red bookmark located on the karyotype. On the right side of the browser window there is a vertical panel with an arrangement of multiple buttons (F):

Scrolling buttons (G): Changes the current view position of the chromosome to the left (<) or right (>).
Zoom in/out buttons (H): Changes the view position to get more or less detail of the viewed area.
Mouse drag action (I): Switches the outcome of the user dragging with the mouse. By default, when the user drags the mouse, the view position is scrolled through the chromosome. However, if the other option is activated, the drag mouse action will highlight the dragged area and zoom in.
Mouse wheel action (J): Switches the outcome of the user spinning the mouse wheel. By default, this will make the user scroll over the web page, but with the other option, the user will make zoom in/out on the area where the mouse cursor is placed.
Tooltips (K): Clicking on this button will display little text boxes with a brief description of each element on the browser interface.
Select chromosome (L): This button will display a list of all the available chromosomes. Clicking on one of them will show it on the browser. By default, the button name is “Chr” but, once that is used, it will change to the name of the selected chromosome.
Search (M): This button will trigger a pop-out window which allows searching genes by position, name, or ID. If the positions forms are not filled, the tool will search in the whole chromosome, while if a range of positions is specified, it will only look for the genes in that range. Through the three tick boxes, the search can be broadened to the GFF genes track (if it is loaded) or to Ensembl IDs and gene names, in case that the genome file is being fetched from Ensembl. Once the search is completed, a new pop-up window with all the matches will appear and, by doing click on one of the matches, the viewpoint will be moved to the position of that match.
Reset focus (N): This button will reset the viewpoint to the default one of the instances.

To get back to the welcome page, users can click on the “Home” button on the top right corner of the browser window (O).

It is important to note that although the browser page allows users to drag and drop correctly formatted files directly into the browser to visualise them, these files will not be saved in the database.

Hands-on Example

Objective: to create a visualization instance for vcf files containing human variant calls from the International Genome Sample Resource (IGSR) and the 1000 Genomes Project repository.

Download vcf files from the IGSR repository

VCF files from IGSR can be downloaded from the FTP site hosted at the EBI ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/.) Both the VCF files and their corresponding indexed files (.tbi) are available to download eliminating the need to index the VCF files for use on CRAMER. To download the following files: “CHBJPT.low_coverage.2010_09.xchr.sites.vcf.gz.” and “CHBJPT.low_coverage.2010_09.xchr.sites.vcf.gz.tbi” type:

$ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot\_data/paper\_data\_sets/a\_map\_of\_human\_variation/low\_coverage/snps/CHBJPT.low\_coverage.2010\_09.xchr.sites.vcf.gz\* _

As already mentioned in the “File requisites” section, VCF files must be compressed and properly indexed with tabix in order to be visualised on CRAMER.

N.B. In the case where a tabix file is not available, it can be generated by running the following command on a compressed vcf file:

$ tabix vcf\_file.vcf.gz

The generated tabix file must be uploaded together with its corresponding vcf file on CRAMER.

2. Create a new instance on CRAMER from Ensembl

Application administrator can log into CRAMER and create new instances or modify existing ones. To create a new instance, go to the welcome page and click the “Sign in” button. This will prompt you to add your credentials. Type your email address and password and press “sign in”. After signing in click on the “Create New Instance” button to open the instance page. Fill out the fields on the form (Fig. 6) to set a name and description for the new instance, select the chromosome to display and set the default starting and end points of view when the instance is displayed on the browser. All these details can be modified later. To fetch the human genome from Ensembl, go to the “Genome” region on the top of the page and hover with the mouse over the three available tabs to see the description of what each does. Click on the first button (e!), to activate it. This option enables you to fetch genomes from Ensembl. Then go to the scroll down menu underneath and select “Human”.

Please note that not all the species genomes on this list can be fetched from Ensembl. The reason for this is that they are are either not available in the database, or that they content is not correctly formatted. A list of Ensembl genomes not currently displayed on CRAMER is avellable in the Appendix.

Next you need to activate the “Ensembl Tracks” to display more information about the human genome. The available Ensembl tracks are “Ensembl Genes”, “Ensembl Sequence” and “SNP database” and their function has been described in the Tracks section. You can either activate all the Ensembl tracks at once or select individual tracks to be displayed.

Fig. 6 Form for new visualization instance on CRAMER

Add local files

Next, we need to visualize the files we have just downloaded in the previous step. In this example we will upload the “CHBJPT.low_coverage.2010_09.xchr.sites.vcf.gz” downloaded from IGSR. To create new VCF tracks follow the steps below:

Go to the “Track” box and activate the “VCF Highlights” tab.
Click on the plus button next to “VCF Highlights”.
Start populating the fields in the pop-up window. The ones marked with an asterisk (*) are mandatory and consist of:
1. Name: Name of the track that is going to be created.
2. Info: Brief description of the track that will be used as a hover label on the browser.
3. URL or Filepath: The url or the filepath of the VCF file.

When the fields have been completed, press “Add Track”.

You can also create a SNP density track by activating the “Add SNP Density Track” and uploading the same VCF file.

Finally press the “Submit” button. This action will take you back to the instance list page. Scroll down and select the name of the instance you just created from the instance list. This will open the genome browser window (Fig. 7) and will display the data for the chromosome and specific region you selected when creating the instance. This information is also contained within the URL link for this page, eg. http://localhost:4000/index?name=Human%20Genome%20Testing&r=X:35938492-35987711 The “r=X denotes chromosome X and 35938492-35987711 is the region currently displayed on the genome browser. The link is updated each time the user performs an action, such as zoom in/out or change chromosome (Please note that the vcf file we downloaded contains only variants on Chromosome X, so if you pick a different chromosome, the visualization instance would work fine, however, the vcf track will contain no SNPs). You can replicate the same view of the genome by copying and pasting the URL link in a new tab on the web browser.

Fig. 7 Screenshot of the Human Genome visualisation instance showing tracks for: Chromosome X and 35938492-35987711

Drag and drop

An alternative way of uploading files on CRAMER is by using the “drag and drop” functionality which permits users to display data on the genome browser page for as long as the instance is displayed. The drag and drop functionality is a convenient way of displaying data without permanently adding them to the instance. Just select files with the proper format and drag them to the browser which will automatically generate the tracks displaying the data for that specific region. To replicate the example above, select both the “CHBJPT.low_coverage.2010_09.xchr.sites.vcf.gz” file and its tabix indexed file “CHBJPT.low_coverage.2010_09.xchr.sites.vcf.gz.tbi” and drag and drop them in the genome browser page. The name of the new track will be the same as the file name. In case you only selected the vcf file, the following error message will appear: “ERROR: GZipped VCF files must be accompanied by a .tbi index file”. Drag and drop can be used for other file types as well.

Explore Data

Once you have uploaded the data, there are a number of actions you can do on the genome browser page to explore the data as described in the “Genome browser page” section. For instance, you can search for a specific gene on a chromosome, e.g. PLAC1 on chromosome X, by first selecting the correct chromosome from the drop down menu and then clicking on the “Search” button and typing “PLAC1” in the name field (Fig. 8).

Fig. 8 CRAMER gene search form.

Then tick the fields “Ensembl gene IDs” and “Ensembl gene names” since the genome is fetched from Ensembl. After clicking on the arrow next to “Search” a list will appear containing information including the gene name and ID and the start and end positions. By clicking on the gene name on ID the browser will resize to display the area containing the gene of interest. For more information on the gene you can click anywhere on the gene schematic on the annotation track and a pop-up window will appear with additional information (Fig. 9). If you click on the gene name on the pop-up window, you will be redirected to the Ensembl webpage for this gene, which will open in a new tab.

Fig. 9 CRAMER gene search result for PLAC1

Common errors

When trying to visualise an instance the following error messages may appear:

“Wrong Content in the Genome File” or “Genome File Does Not Exist.” and/or “the instance is blank”.

This error can be caused by:

A complex chromosome name such as “genescaffold:gadMor1:GeneScaffold_3590:1:3911206:1 REF”

The chromosome positions have not been correctly established on the instance details.
An incorrect URL/Filepath

When uploading a VCF file, the following error may appear: “ERROR: Gzipped VCF files must be accompanied by a .tbi index file”

This error means that the VCF file is not properly compressed.

In the genome browser page a warning may appear after you perform the drag and drop operation: “Data for this track is not displayed in regions greater than 100.00 kb”.

To remove this warning press the "zoom in" button repeatedly.

Appendix

Requirements for the correct display of imported files

The genome file needs to be in JSON Object format. The file needs to respect some requirements:

start with ‘Genoverse.Genomes.’ and then the name of the genome;
contain the name of the chromosome such as “1” or “MT”;
in the chromosome element, the size and the bands are required. The size is the length of the chromosome and the bands can be filled with a list to display the karyotype.

Below, there is an example of the genome file for the tomato:

Genoverse.Genomes.tomato = {

"1": {

"size": 98543444,

"bands": []

},

"2": {

"size": 55340444,

"bands": []

},

"3": {

"size": 70787664,

"bands": []

}

};

List of Ensembl Genomes not currently available to display

(As of 20.10.2019)

Genome files not available

Alpaca, Algerian Mouse, Armadillo, Black snup-nosed monkey, Chinese Hamster CriGri, Chinese softshell turtle, Cod, Coelacanth, Coquerel's sifaka, Damara Mole Rat, Dolphin, Flycatcher, Hyrax, Lesser hedgehog tenrec, Marmoset, Shrew, Sloth, Sooty Mangabey, Tarsier, Tilapia, Tree Shrew, Upper Galilee, Wallaby.

Genome file exists with wrong content

Amazon Molly, Angola Colobus, Bolivian Squirrel Monkey, Brazilian Guinea Pig, Bush baby, C. Savignyi, Capuchin, Cave Fish, Chinese Hamster CHOK1GS, Cow, Degu, Drill, Elephant, Ferret, Fugu, Golden Hamster, Golden snub nosed monkey, Guinea Pig, Hedgehog, Horse, Kangaroo rat, Lamprey, Lesser Egyptian Jebroa, Long-tailed chinchilla, Ma's night monkey, Medaka, Megabat, Microbat, Naked mole rat female, Naked mole rat male, Northern American Deer Mouse, Panda, Pig tailed macaque, Pika, Platyfish, Squirrel, Stickleback, Tasmanian Devil, Xenopus.

References

1. Genome Research Limited. tabix manual page. 2018. http://www.htslib.org/doc/tabix.html. Accessed 29 Apr 2018.

2. Genome Research Limited. samtools manual page. 2018. http://www.htslib.org/doc/samtools.html. Accessed 29 Apr 2018.

3. The Bioconda Team. Using Bioconda — Bioconda documentation. 2016. https://bioconda.github.io/. Accessed 28 Apr 2018.

Name		Name	Last commit message	Last commit date
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Wiki/Images		Wiki/Images
bin		bin
config		config
example_database		example_database
indexes		indexes
media		media
models		models
public		public
routes		routes
views		views
.DS_Store		.DS_Store
.env		.env
.gitignore		.gitignore
Dockerfile		Dockerfile
README.md		README.md
app.js		app.js
list-js.js		list-js.js
package-lock.json		package-lock.json
package.json		package.json
processingBAM.sh		processingBAM.sh
webpack.config.js		webpack.config.js

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The Cranfield Genome Browser - CRAMER

Introduction

Table of Contents

How to install CRAMER

Dependencies

Install CRAMER on Linux

Option 1: Docker-based installation

a. Run CRAMER using pre-built docker image

b. Build a new docker image based on the latest git version

Docker-based installation (MacOS)

Option 2: Manual installation

CRAMER workflow

File requisites

How to create a new user account

Sign in

Tracks

Plugins

How to navigate CRAMER

Welcome page

Genome browser page

Hands-on Example

Download vcf files from the IGSR repository

2. Create a new instance on CRAMER from Ensembl

Add local files

Drag and drop

Explore Data

Common errors

Appendix

Requirements for the correct display of imported files

List of Ensembl Genomes not currently available to display

Genome files not available

Genome file exists with wrong content

References

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