KewinOgink

Hi, I don't understand how the ROC Precision recall curve can be made with other metrics. As I understand the --roc switch to feature on must be in the query...

**Describe the issue** Hi, I am working with really large VCF files (millions of variants). I didn't see a way to parallelize snpeff, so I wanted to split my vcf...

test sequence not as expected?

3

Related to the https://github.com/marbl/ModDotPlot/issues/29 I thought to investigate by using test sequences. I take a sequence from arabidopsis chr1 and copy paste a sequence 3 times, ``` %%writefile ../tmp/seq1.fa >seq1...

Hi thanks for the great tool! I am testing it and I noticed a difference and it got me confused. I looked at https://github.com/marbl/ModDotPlot/issues/22 but it I downloaded moddotplot last...

missing space in mm2 params crashes

1

when you use mm2 params, I notice it crashes: turns out this is because of a missing space that's not added here: https://github.com/agshumate/Liftoff/blob/94d6073ee2400c438d181a67d3af1e362197d839/liftoff/run_liftoff.py#L167 ``` @SQ SN:Chr20 LN:52064518 @SQ SN:ChrUn LN:1868102...

``` lifton -t 32 -copies -cds -polish -g ref.gff3 target.fa ref.fa ==================================================================== An accurate homology lift-over tool between assemblies ==================================================================== ██╗ ██╗███████╗████████╗ ██████╗ ███╗ ██╗ ██║ ██║██╔════╝╚══██╔══╝██╔═══██╗████╗ ██║ ██║ ██║█████╗...

Hi I notice that when I have gene duplicates that are identical to each other, only 1 has a hit in my target genome and the rest are unmapped. I...

Hi, thanks for your really nice tool. I lift over my gff to multiple genomes. I noticed that a transcript in genome A is missing the matches_ref_protein annotation in the...