ExplorATE - Data Test

Overview

This folder contains the dataset to run the ExplorATE vignette.

Model organisms data

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humans data set

The inputs_hs directory contains simulated data from a human ovary sample. The reads subdirectory contains a subset of .fastq files from the original data set. Additionally, it includes a de novo transcriptome (trme_hs.fa) and a transcriptome-derived RepeatMasker file (RM_trme_hs.out).

Drosophila melanogaster data set

The inputs_dm directory contains a data set for Drosophila melanogaster based on Ohtani et al. (2013). This directory contains the files: geneModel_dm.gtf, a gene model for the D. melanogaster genome (v3) genome_dm.fa, a reference genome (v3) RM_gen_dm.out, a genome-derived RepeatMasker file RM_trme_dm.out, a RepeatMasker file derived from the transcriptome trme_dm.fa, a de novo transcriptome for the data set

Users can download reads in .fastq format from Gene Expression Omnibus (accession no. GSE47006). See the ExplorATE vignette.

Non-model data set

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Liolaemus parthenos data set

The inputs_lp directory contains a subset of Liolaemus parthenos data. The complete data set is available in Gene Expression Omnibus (accession no GSE173261). The directory contains: reads, a folder with the reads in .fastq (subset) format blastAnot_lp.outfmt6, a BLAST output, in output format 6, for the de novo transcriptome geneModel_lp.gff3, a TransDecoder output file RM_lp, a RepeatMasker file for the de novo transcriptome (subset) trme_lp, the de novo transcriptome (subset)

How to use

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Clone the repository to the desired directory with the following command.

git clone https://github.com/FemeniasM/ExplorATE_data_test

Access the desired data set and unzip the files with the following

gzip -d *.gz

User guide and vignette

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Check the vignette and the user guide for more information.