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tianshilu / QBRC-Somatic-Pipeline

QBRC Somatic Mutation Calling Pipeline
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Does it work with 10x scRNA-seq BAM ? #12

Open lwtan90 opened 2 years ago

lwtan90 commented 2 years ago

Hi,

I am just wondering if this work flow works with 10x data?

Wilson

wtwt5237 commented 2 years ago

Yes.

Please see our paper for the tunings that are needed to make it work better on 10x data: Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data

Tao

SuqinYang commented 2 years ago

Hi，@wtwt5237 Can it be used in scATACseq variants calling?

wtwt5237 commented 2 years ago

@SuqinYang

we haven't tested. but I think so. It's better than scRNA-seq actually

SuqinYang commented 2 years ago

Thank you!

Best wishes!

SuqinYang commented 2 years ago

Hi,@wtwt5237 Sorry to trouble you.I am trying to use the "QBRC-Somatic-Pipeline" with 10X scRNAseq data.We know that the 10x Genomics single-cell sequencing platform outputs the raw sequencing reads of all cells in one Fastq file. The ScSplitter is used to split the reads using their cell barcode. But I have a puzzle, if I have a normal sample and a tumor sample, both of which use ScSplitter to split a large fq file into small fq files, (if I understand correctly, the QBRC-Somatic-Pipeline is equivalent to calling variants to individual cells), how do I pair cells from the tumor with cells from the normal in the somatic.pl?

wtwt5237 commented 2 years ago

Hi @SuqinYang

It might make more sense to use the "germline-only" mode of our variant calling pipeline, which would not need to pair cells.

Thanks!

Tao