Aligning to b37 vs hg19

[esh81]

Hi, I'm using the test datasets to try to run this pipeline and have had to do some troubleshooting because of the hg19 vs b37 resources listed on the scATACseq_mtSMC_3.yaml. I first tried the 1_scATAC_mito.sh with all the same resources as on your yaml file (except the MTIndel file, because I couldn't seem to find the exact one online), and I ran into the trouble because hg19 and b37 have a difference in the chromosome naming convention (chr1 vs 1). I've tried multiple combinations of things, and now I'm down to the dbSNPs and ref_TSS file being hg19 and everything else being b37 and finally got the 1_scATAC_mito.sh to run all the way through but there are no reads for genomeQ30PE_reads or Total_TSS_reads or mtQ30PE_reads. Could you shed some light as to how you resolved the hg19 vs b37 mix of resources?

Thank you!

[marvinquiet]

Same here! I am running into the same problem.
Did you solve it?

Sincerely,
Wenjing