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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
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Reproducing cellranger count from bamtofastq #24

Closed mxposed closed 3 years ago

mxposed commented 3 years ago

Thank you for the tool.

Before including it in our analysis pipeline, I wanted to give it a quick check, and set up this:

— we have a small sample processed with cellranger 3.1 — run bamtofastq on this sample possorted.bam — run cellranger on bamtofastq output — compare original and restored matrices.

Unfortunately, they are not identical. In the filtered_feature_bc_matrix I see a small difference in barcodes.tsv.gz for example. I wonder, what is causing this and how to debug it?

mxposed commented 3 years ago

Sorry for disturbance, I found out that I used different reference genome for the second run. When I used the same reference genome as for the original run, the results were identical. Thank you