xiekunwhy

When I use gffread, I got duplicate mRNA errors, sed 's/Target_ID/ID/g' uniref90.gff > uniref90.ID.gff gffread uniref90.ID.gff -g ../Op-f.pctg.mask.fa -x uniref90.ID.cds.fa -y uniref90.ID.pep.fa GFF Error: duplicate/invalid 'mRNA' feature ID=Ofa004732 And Ofa004732...

Hi, I see what you mean, thank you for your reply. Best, Kun

Thank you for your reply, I am not so familiar whith them, and I am now trying them, I will make a PR if some of them have a good...

Hi, The paper of pin_hic and endhic have been published. pin_hic: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04453-5 endhic(preprint): https://arxiv.org/abs/2111.15411 endhic has a better performance than others if N90 is longer enough, in my opinion. Best,...

+1 but the developers have no plan to do that, https://github.com/cole-trapnell-lab/monocle3/issues/501 https://github.com/cole-trapnell-lab/monocle3/issues/187 https://github.com/cole-trapnell-lab/monocle3/issues/174

Any one solved this problem?

Hi @KatharinaHoff , Thank you very much for your reply, and I understand now. Best, Kun

You may try to prepare hints file yourself. /path/to/Augustus/bin/bam2hints --in=align.bam --out=bam2hints.gff perl /path/to/BRAKER/scripts/filterIntronsFindStrand.pl ref.fa bam2hints.gff --score > fixed_hintsfile.gff 2> error.gff Don't forget --score option when running filterIntronsFindStrand.pl (very important). Best,...

+1 Diamond v2 is faster and more sensitive than last, and is the best tool for nr searching maybe. So add diamond support is a good suggestion I think.

Hi, The expected genome size is ~3.2G accorrding to FCM results, but it is a high heterouzygous genome(only heterouzygous peak in kmer curve plot). The following is the file sizes...