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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Obtain fastQ file from .bam files #201

Closed pmarzano97 closed 8 months ago

pmarzano97 commented 1 year ago

Hello world! I'm trying to process public .bam files to obtain fastQ files.

I've downloaded the files from the ENA browser (for example https://www.ebi.ac.uk/ena/browser/view/ERR3804256), and I've obtained a file named "WSSS8062674.bam". Then, I launched on the terminal the command "cellranger bamtofastq" but this error came up: "bamtofastq v1.4.1 WARNING: no @RG (read group) headers found in BAM file. Splitting data by the GEM well marked in the corrected barcode tag. Reads without a corrected barcode will not appear in output FASTQs Unrecognized 10x BAM file."

How can I proceed with the processing? Is there a way to fix this issue? Do I need to rename the file .bam or something different that I can do? My goal is to convert it to fastQ to do the CellRanger count command and obtain a file on which I can work. The authors processed the files I would like to analyze with CellRanger 2.1.0, but did not upload the fastQ files, only the .bam ones.

Thanks all!

elehnert10x commented 8 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.