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10XGenomics / scHLAcount

Count HLA alleles in single-cell RNA-seq data
MIT License
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Error: chr name of BAM file, '6' vs 'chr6' #22

Closed wu-yc closed 2 years ago

wu-yc commented 2 years ago

Thanks for this fantastic pipeline. It is really a useful tools. When testing on my own data, those errors were generated:

07:21:50 [INFO] Reading database index from disk 07:21:50 [INFO] Finished reading index! 07:21:50 [INFO] Mapping reads from BAM to database Failed with error: Error fetching locus 6 from BAM file. Are you using a valid contig name? Check for '6' vs 'chr6'. Additional details :Fetch

Error fetching locus 6 from BAM file. Are you using a valid contig name? Check for '6' vs 'chr6'.

It seems that this is caused by the fastq alignment to GENCODE or ensemble reference. I used the 10x cellranger official refdata-gex-GRCh38-2020-A as the reference genome. Any easy-to-use suggestions?

Thanks again for this beautiful package.

Best, Yingcheng

wu-yc commented 2 years ago

My current solution is to modify the BAM file chr names by using samtools reheader. And it seems to be working.