Hello! Is there a standard method to subset the bam file from cellranger with seurat_clusters? #8452
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Hello! I was wondering if there was a "standard" method for doing this? I found this blog that was very helpful and I think it would be a really good idea and feature for looking at the frequency of your UMI and then even reads for low expressed DE UMI, with the UCSC genome browser. So I wanted to subset by the SCT clusters and then the integrated clusters from the raw bam file. If you have any ideas or comments they are greatly appreciated. Here is the blog URL, https://divingintogeneticsandgenomics.com/post/split-a-10xscatac-bam-file-by-cluster/ Thanks! |
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Replies: 1 comment
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Couple of tools (I would also note that just from very Quick Look I think that blog post should also be applicable to GEX BAMs too). 10XGenomics/subset-bam#17 (comment) https://github.com/10XGenomics/subset-bam https://github.com/timoast/sinto Best, |
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Couple of tools (I would also note that just from very Quick Look I think that blog post should also be applicable to GEX BAMs too).
https://kb.10xgenomics.com/hc/en-us/articles/360022448251-How-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes
10XGenomics/subset-bam#17 (comment)
https://github.com/10XGenomics/subset-bam
https://github.com/timoast/sinto
Best,
Sam