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JiekaiLab / scTE

MIT License
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Hidden Dependency on SAMtools and Question Regarding STARsolo Runs #50

Open ColeWunderlich opened 1 year ago

ColeWunderlich commented 1 year ago

It appears the code base has a hidden dependency on samtools. Every run I attempted produced the following error:

bam has no cell barcodes information, plese make sure the aligner have add the cell barcode key, or set CB to False

untill I installed samtools on my system. Only then was I able to pass the CB/UMI check. It looks like samtools is being called from here among other places.

You may want to add this to your installation instructions so that users are aware.

I also had a question regarding the recommended settings for running STARsolo. In the readme, you recommend -CB CR -UMI UR for STARsolo but recommend -CB CB -UMI UB for Cell Ranger. Is there any reason you recommend raw/uncorrected tags for STARsolo but corrected tags for Cell Ranger? In general which tags are best to use?

jphe commented 1 year ago

Yes, scTE requires samtools.

It has no corrected tags for old version of STARsolo, we recommend -CB CB -UMI UB for the latest STARsolo and Cell Ranger output bam file.

ColeWunderlich commented 1 year ago

Ok, thank you!