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Problem with downloaded 10x Genomics from GEO (SRA) #2

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shenghuanjie opened this issue Nov 5, 2019 · 1 comment
Open

Problem with downloaded 10x Genomics from GEO (SRA) #2

shenghuanjie opened this issue Nov 5, 2019 · 1 comment
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rnaseq issues realted RNA-seq both bulk and single cell

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@shenghuanjie
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shenghuanjie commented Nov 5, 2019 •
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While extracting bam files from SRA, there might be a problem if you use the standard commands from samtools.
For example, in this dataset, if you run:

sam-dump SRR8895023 | samtools view -bS - > SRR8895023.bam

It will not get the original 10xBAM file with required headers for Cell Ranger to perform the alignment.
This is also mentioned here:
'Invalid BAM record: read: "1" is missing tag: "CR"'
@shenghuanjie
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It turns out that you need cellranger from 10x to work with their data.

@shenghuanjie shenghuanjie added the rnaseq issues realted RNA-seq both bulk and single cell label Nov 11, 2019
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