Josh Burton

Wow, thank you so much for the quick and thorough explanation! I didn't realize you were cross-developing between GraphAligner and verkko, but it totally makes sense.

Sure! I'm using minimap version 2.24-r1122. Here's my minimap2 command: `minimap2 -ax splice:hq -N10 --MD ` Here's the output bam file that corresponds to the paf file I sent before:...

Here's [MHC.gff.gz](https://github.com/baoxingsong/AnchorWave/files/14004238/MHC.gff.gz). This is the gff file I used to derive the anchors fasta file I sent earlier (MHC.anchors.fa). It's a subset of the genome-wide gff file at https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz.

Is there a reason why I should not be including non-coding genes in my anchors fasta file? Right now I'm including the CDS sequence if it's available but also including...

Aha - thank you for that tip! You're absolutely right, I did not use `anchorwave gff2seq` to make my `MHC.anchors.fa` file. Instead I parsed the GFF manually. I did this...

Thanks, this is really helpful to know! I tried tweaking my script to generate anchors files, so that it ignores exons and CDS's of length

Which results are you trying to repeat? The creation of the anchors fasta file from the GFF, or the creation of the alignment paf file using `anchorwave genoAli`?