No access to Mappability file and cell specific bam files

[kzb193]

Hello,

I am working with a scWGS bam file generated using the cell ranger DNA pipeline, and I would like to use SEACON. Can you please help with the following two issues?

1. Do I need to split this bam files into cell specific bam files (as described in 'Sequencing reads' subsection under 'Inputs and Preparation') ?
2. How can I obtain the corresponding (hg19) required Mappability file? Can you please give some suggestions? I was unable to access the google drive link provided.

Thanks.

[samsonweiner]

Thanks for your interest in SEACON! Here are some solutions to your issues:

1. As of right now the input requires cell specific bam files. 10x genomics offers a tool to split a single barcoded bam file into cell specific bams, found here: https://github.com/10XGenomics/subset-bam.
2. Sorry to hear the google drive link was not working, it no longer works on my end either. To make things easier, we have uploaded the mappability files for both hg19 and hg38 to zenodo, which can be downloaded from https://drive.google.com/drive/folders/1vKk07qLjfKS3elvzAvXMBS0ZV3UqNVi2?usp=drive_link. For convenience I used liftover to convert the same hg38 mappability file into hg19 coordinates, so let me know if you experience any other troubles. If you want, you can download a custom bigwig file for hg19 directly from ucsc (https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability).