search

sridnona / cb_sniffer

mutation(barcode) caller for 10x single cell data
GNU General Public License v3.0
44 stars 16 forks source link

cb_sniffer in scATAC data? #17

Open AmosFong1 opened 3 months ago

AmosFong1 commented 3 months ago

I am working with 10X Multiome data, and I was able to run cb_sniffer on my GEX bams. However, running cb_sniffer on my ATAC bams with the same barcodes and variant files for the successful GEX runs, gives me no results (only headers printed in *_counts_CB.tsv and *_counts_UB.tsv. I was wondering if this is expected or have I made an error? Is there anything that needs to be adapted to accommodate cb_sniffer runs using ATAC data?

AmosFong1 commented 1 month ago

@sridnona bump

sridhar0605 commented 1 month ago

Hey @AmosFong1 , Thanks for tagging, sorry i did not get the initial issue alert. I dont think i have tested this on scATAC data. Do you have demo data that you could share as a tar file? (the variant call file and bamfile)

AmosFong1 commented 1 month ago

Hello @sridhar0605 here is some dummy data. It seems GitHub doesn't accept tar so I used gzip, and the bam file should only contain 20 reads: dummy_variant_file.txt dummy_bam_file.bam.gz

Please let me know if anything else is needed from me