Open xiekunwhy opened 2 years ago
There was a problem in training. Your HMM can't make initial exons.
Hi,
I used following commands to run training and it seems that every things worked OK, I don't known why hmm file has problem,
perl gff3_to_zff.pl -g mikado.keep3.gff -f Op-f.pctg.fa -o mikado.keep3.zff fathom mikado.keep3.zff Op-f.pctg.fa -validate > validate.log perl cleanZff.pl -z mikado.keep3.zff -l validate.log -o mikado.keep3.clean.zff fathom mikado.keep3.clean.zff Op-f.pctg.fa -categorize 1000 > categorize.log fathom uni.ann uni.dna -export 1000 -plus > uni-plus.log mkdir params cd params forge ../export.ann ../export.dna > ../forge.log perl hmm-assembler.pl Op-f params > Op-f.hmm
Best
Maye the gff3_to_zff.pl script gives a wrong guide, it only produce Exon region.
It might be a good idea of we did a zoom. Send me your availability.
From: @.> Sent: Sunday, December 26, 2021 6:37 PM To: @.> Cc: Ian @.>; @.> Subject: Re: [KorfLab/SNAP] SNAP produced a long long long gene(~40M)? (Issue #13)
Maye the gff3_to_zff.pl script have a wrong guide, it only produce Exon region.
— Reply to this email directly, view it on GitHubhttps://github.com/KorfLab/SNAP/issues/13#issuecomment-1001299170, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAI6KN4FO4OGJK5X5PWOGQLUS7GQJANCNFSM5KYXHVMA. You are receiving this because you commented.Message ID: @.***>
Here is my script, but I need to read all gtf and fasta file to RAM. gtf2zff.zip
And here is snap zff to gtf script,those who want gff can use gffread to convert gtf to gff snap2gtf.zip
Hi,
SNAP ofthen give some strange results, for example, output a long long long gene, the length of the gene cover almost the whole scaffold, why and how to avoid that?
Here is the hmm file I used and the result file SNAP output.
snap.zip
Best, Kun