Question: scRNAseq: Split FASTQ into cell specific FASTQ Files
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gravatar for niklas.lang
4 weeks ago by
niklas.lang0 wrote:

Hi ! I did scRNAseq (10XChromium) of cancer cells and now I am looking for a simple way to split my FASTQ Files into celll specific FASTQ Files. Alternativley split my BAM File into cell specific BAM Files - because I need one FASTQ (BAM) File per cell in order to do perform variant calling on the single cell level. My goal is to obtain one single VCF file per cell.

Is there a build-in function in CellRanger for that? Are there any other tools to demultiplex my FASTQ/BAM Files using cell barcodes and split them into cell specific FASTQ/BAM Files?

Any help is highly appreciated! Thank you so much!

ADD COMMENTlink written 4 weeks ago by niklas.lang0

It is incredibly unlikely that this will prove useful. 10X reads will be enriched around the polyA site and be highly redundant.

ADD REPLYlink written 4 weeks ago by Devon Ryan90k

My idea was to split the BAM File into several cell-specific BAM File by using the "CB" Tag. I don't know how this could possibly interfer the PolyA enrichment, so I would be glad to hear what your concerns are?

ADD REPLYlink written 29 days ago by niklas.lang0

The question is whether single cell variant calling with this type of data is likely to be useful. The answer is "no", because you're mostly sequencing around the TES.

ADD REPLYlink written 29 days ago by Devon Ryan90k
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