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gxiaolab / scAllele

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Input bam? #4

Open cnk113 opened 2 years ago

cnk113 commented 2 years ago

Hello,

This is a great tool, I was wondering if it was possible that a single BAM file could be inputted but separated by cell barcode as a tag?

Thanks, Chang

giovanniquinones commented 2 years ago

Hi Chang, As of now, scAllele does not do that. This is a good feature to implement however, and will be incorporated in upcoming versions.

jjializhu commented 2 years ago

Hello, I was very interested in scAllele, but frustrated by the huge amount of data, any good tips on how to save time and space to split BAM files when scAllele is performed on thousands of cells Separately.

giovanniquinones commented 2 years ago

Are you using 10X data?

jjializhu commented 1 year ago

yes

jgarces02 commented 1 year ago

I'm planing to use scAllele on 10X (3') data, is it feasible? Reading this issue, any advice for using the 10X's BAM as input? Thanks

giovanniquinones commented 1 year ago

unfortunately, we only tested scAllele in Smartseq2 data. You could split the 10X bam into cell-specific individual bams. Given the low coverage for individual cells, it should run pretty fast on each one, but there'd be very limited detection of events.

jgarces02 commented 1 year ago

Perfect, thanks for your answer. My question was more related to the short read length of 10X tech (in addition to being 3' and, consequently, polyA).