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kharchenkolab / dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data
GNU General Public License v3.0
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Config file for 10X single-cell V1 chemistry #30

Open hnakhoul opened 6 years ago

hnakhoul commented 6 years ago

Hello--I'm testing dropEst on a dataset generated with the 10X V1 chemistry (https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing-requirements-for-single-cell-3). It seems that the V2 chemistry is the one that's specified in the 10x.xml file, and the necessary changes for V1 data aren't obvious to me.

Naively trying

barcode1_length: 0 barcode2_length: 14 umi_length: 10 r1_rc_length: 0

in the config.xml seems to stall at the reads per UMI per gene estimation step. I'd appreciate any advice you might have!

VPetukhov commented 6 years ago

Hello, Sorry, but currently there is no way to run droptag on 10x v1.

uzairray275 commented 1 year ago

I need V1 chemistry file for 10x kindly anyone share with me that file