german nudelman

sambamba-markdup: Unexpected '-' when converting from type string to type ulong

1

I'm getting this error using sambamba/0.5.6 on centOS 7. "sambamba-markdup: Unexpected '-' when converting from type string to type ulong" my command is: sambamba markdup -t --tmpdir $tmpdir $filtered.sorted.bam undup.bam...

Thanks for the tool, it is very useful. I now have the need to apply NGSCheckMate on the mouse data. While I found the the SNP bed file for Human...

checkchrom doesn't seem to work for me

1

My GTF have chromosomes names like GL00000*.* here is cmd I use: $ python /path/to/leafcutter/clustering/leafcutter_cluster_regtools.py \ -j path/to/Aligned.sortedByCoord.out.bam.junc \ -m 50 -o \ -l 500000 \ --nochromcheck=checkchrom Even though I...

local variable 'genes2' referenced before assignment

4

* spladder version:3.0.4 * Python version:3.8.15 * Operating System:CentOS ### Description I was trying to optimize a run a large cohort by using the "--chunked-merge" mechanism. I first generated the...