Ben Berman
Ben Berman
> Can you post the SAM entries for those 6 reads? I attached them at the bottom of the original message, file called "problem.hg38.sam.txt"
I believe Pysam is 0.15.3 Regarding the origin of these, it could have to do with a problem with the trimming (in this case soft clipped by DRAGEN aligner). It...
I am going to look into why our DRAGEN alignments are clipped like this, and I will also look at BWA alignments of the same reads, or if it's due...
My mistake on the properly paired flag, I remembered that wrong. People do hard clipping for a variety of library-specific reasons. For instance, Swift makes the most popular single-stranded kits...
I just wanted to note that I have the same problem publishing directories on Az storage. Environment: Nextflow v.23.04.0 Storage: Hierarchical Namespace (Datalake Gen 2) I assume this will be...
I would really like this as well! Especially for `input` and `outdir` parameters which change for every launch.