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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Feature MEX file output incorrect #155

Closed lmogil closed 8 months ago

lmogil commented 2 years ago

I recently upgraded to cellranger version 6.1. and discovered that the feature file contains quotations around each row. This posses issues for post processing. I have resolved this manually but is there a way to get this addressed in the software package? Example of a line in the file: "ENSG00000223972.5 DDX11L1 Gene Expression"

evolvedmicrobe commented 2 years ago

Which feature file are you referring to?

lmogil commented 2 years ago

in the filtered MEX output. the file is called feature.tsv.gz. its one of three files in for analysis along with barcodes.tsv.gz and matrix.mtx.gz

lmogil commented 2 years ago

referred to here on the site https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

evolvedmicrobe commented 2 years ago

I just check a few of our example datasets and didn't see the quotes in that file when I unzipped it, do you observe this with any of our example datasets?