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Published 20 hours ago • verified publisher icon liulab-dfci

Hashed samples in 10X

Open learning-MD opened this issue 2 years ago • 2 comments

Hi, first of all, thank you for this fantastic resource!

I have 5' scRNA-seq data on PBMCs from 40 patients that have been hashed with antibodies - 5 samples tagged and run in a lane. Are there any specific adjustments that need to be made before running TRUST4 on the large BAM file (or FASTQ files) of these hashed samples?

Thanks in advance!

learning-MD avatar Aug 07 '22 20:08 learning-MD

I don't think there will be a problem with that. The memory usage might be large due to the run contains immune repertoires from 40 samples.

Just curious, is there a mapping to know which barcode corresponds to a sample or patient? Thanks.

mourisl avatar Aug 08 '22 02:08 mourisl

Thanks! Yes, there are feature barcodes to identify what corresponds to what sample. I think I'll just have to run one hashed sample to see how it works out and take it from there.

learning-MD avatar Aug 08 '22 23:08 learning-MD