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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Reanalyze older BAM? #78

Closed J-Moravec closed 4 years ago

J-Moravec commented 4 years ago

Hi, I have BAM file from the 10X cellranger count analysis and i would like to use it for GATK SNV pipeline. However, since this is an older experiment, I don't have the original reference genome available so I need to remap is again my transforming back to fastq and mapping it with a new reference genome.

This, however, wipes out all the sweet 10X BAM tags, such as the incredible important CB tag for distinguishing individual cells.

This brings me to my question: Is there a way to reanalyze older BAM files without access to the raw input from sequencer? I tried to look at the description of pipeline and even at the code, but its not as neatly described as I would like to. I know that STAR is involved and that there is bamtofastq https://github.com/10XGenomics/bamtofastq involved there, but can't figure out the order.

Thanks, -- Jirka

evolvedmicrobe commented 4 years ago

Hi Jirka,

Indeed, bamtofastq is the tool for this job, since it takes a file with alignment information (the BAM) and produces one without it (FASTQ), you shouldn't need to worry about how STAR added in that alignment information.

Please contact: support@10xgenomics.com if you need any more help.

Cheers, N