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10XGenomics / scHLAcount

Count HLA alleles in single-cell RNA-seq data
MIT License
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run error #20

Closed khksw0403 closed 2 years ago

khksw0403 commented 2 years ago

error

Hi, folks.

I'm trying to use this module on scRNA analysis but faced a little bit of trouble. tried several kinds of combinations but showed the same pattern as the attached files. smatools sort, samtools redeader etc

Thanks,

khksw0403 commented 2 years ago

resolved it: samtools view -@ 7 -h /path/bam_file | sed 's/chr//g' | samtools view -Shb - -o /path/bam_new_name