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pachterlab / BGP_2023

BSD 2-Clause "Simplified" License
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Error: technology string must contain two colons (:), none found: "10XATAC" #1

Closed tdfair closed 1 year ago

tdfair commented 1 year ago

Hi,

Thanks for adding 10X ATAC-seq support to kb, I'm trying a command similar to this one (kb_python 0.27.3 installed):

!kb count \ -i peaks.idx \ -g t2g.txt \ -x 10xATAC \ -o out \ -w 737K-cratac-v1.txt \ -t 2 \ --h5ad \ CB.fastq.gz R1.fastq.gz R2.fastq.gz

which raises the error 'technology string must contain two colons (:), none found: "10XATAC"'

Is there a publicly available version of kb_python (or kallisto) that supports this technology?

Many thanks!

sbooeshaghi commented 1 year ago

Hi Tyler- thanks for the question. What I recommend is passing a custom technology string to the -x option in a manner that specifies the barcode and reads. This would look like

0,0,16:-1,-1,-1:1,0,0,2,0,0

For more information about the technology string see: https://pachterlab.github.io/kallisto/manual

I hope that helps!