Jessen Bredeson

Hi, Is it possible that the pipes in your file names are causing the trouble? Otherwise, I've found setting `-f0.0` to work around gaps, where (simple sequence) repeats may be...

Hi @arangrhie, Just a quick note regarding point (i): The plant genome I'm working with is three generations in-bred and was confirmed to be ~93% homozygous by multiple methods, so...

Hi! I'm so glad I found this open ticket. I would like to suggest adding the weighted statistics as options for `bedtools merge` as well. This would be super useful....

I'm seeing something similar. All (-)-strand reads have two or more nts upstream of their indel, reversed with respect to those on the (+)-strand: In the following alignment: GC_C_CG .....

Your recommendation helped me get past my previous error, thank you. Now, however, I am receiving the following error: ``` [M::hk_map_read] read 218057034 pairs [W::hk_sd_ploidy_XY] no sex chromosomes (identified by...

Ah, and the `-hist` function does this as well.

Also with `-polish` as well. Thanks for the tip!

Here is snippet of `CrossMap gff` output: ``` Chr1 Gnomon CDS 6570547 6571454.0 . - 2 ID=cds7;Parent=rna7;Dbxref=GeneID:105946420,Genbank:XP_012811597.1;Name=XP_012811597.1;gbkey=CDS;gene=LOC105946420;product=vomeronasal type-2 receptor 26-like;protein_id=XP_012811597.1 Chr1 Gnomon exon 6601814.0 6601938.0 . - . ID=id41;Parent=rna8;Dbxref=GeneID:108645644,Genbank:XM_018090861.1;gbkey=mRNA;gene=LOC108645644;product=G-protein coupled...

Thanks!

And to answer your question about whether it's in my input file, I ran the following awk one-liner to check and it doesn't seem to be: ```bash $ awk 'BEGIN...