search

chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
106 stars 37 forks source link

gtf -strand convert to + strand #45

Open zlc289 opened 3 years ago

zlc289 commented 3 years ago

Hi, I have a problem when I convert my gtf file to + strand file. I do not what length I should enter. Total length of reference gene or whole length of genome. Because my gtf file is download for whole genome. when I enter reference gene length, the location in + strand file is minus "-". Here is my gtf file. Thanks. AT5G13480_2_cds.txt

singing-scientist commented 3 years ago

Greetings! Thanks for using SNPGenie. The total length of the FASTA (i.e. the whole reference sequence, whether it is a contig, chromosome, or genome) should be used. Let me know if that helps!

zlc289 commented 3 years ago

Thank you for quick response. It is working.

From: Chase W. Nelson @.> Sent: Thursday, April 22, 2021 12:11 PM To: chasewnelson/SNPGenie @.> Cc: Zhou, Lichun @.>; Author @.> Subject: Re: [chasewnelson/SNPGenie] gtf -strand convert to + strand (#45)

CAUTION: External Sender

Greetings! Thanks for using SNPGenie. The total length of the FASTA (i.e. the whole reference sequence, whether it is a contig, chromosome, or genome) should be used. Let me know if that helps!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchasewnelson%2FSNPGenie%2Fissues%2F45%23issuecomment-824979067&data=04%7C01%7CLichunZhou%40uky.edu%7C4afa344206b64e63cfda08d905a9468a%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637547046852974050%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6zJfA2nrKPplLIq8EvzCy5w%2FXjqxrQ%2BySm64tr0cJiQ%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAPP4UJVRR2C762FYY2SEW6LTKBDCXANCNFSM43MYX3BQ&data=04%7C01%7CLichunZhou%40uky.edu%7C4afa344206b64e63cfda08d905a9468a%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637547046852984045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=oyCi7aI6Pktao9gDFtjxWckFDisA4bN0kZZ6Q%2F1rpcU%3D&reserved=0.