Braker2: Acquiring Transcript/EST data for a de novo genome

[DustinSokolowski]

Hello!

Thank you for the great bioinformatics workbook. I've been using the Braker tutorial as inspiration to annotate me own de novo genome and it's been quite helpful this far.

I am trying to generate the transcript/EST information as part of the (required?) input for Braker2. Is the Transcript/EST information a different datatype entirely than RNA-seq, and if I don't have it then this step must be skipped? Or can it be generated from the RNA-seq data?

I was thinking that if it can be generated then perhaps I'd generate a gtf file with stringtie/guided trinity, pull the fasta file from that with bedtools, and then re-align the fasta to the genome. This being said I may be way off-base and missing something obvious.

If you have any advice here then that would be very valuable!

Best,
Dustin

[remkv6]

Hi Dustin, The EST’s/transcripts are not required, though using Uniprot (manually curated) proteins will improve your prediction. You can absolutely skip it. Good luck! Rick From: Dustin Sokolowski ***@***.***> Sent: Tuesday, March 15, 2022 4:40 PM To: ISUgenomics/bioinformatics-workbook ***@***.***> Cc: Subscribed ***@***.***> Subject: [ISUgenomics/bioinformatics-workbook] Braker2: Acquiring Transcript/EST data for a de novo genome (Issue #64) Hello! Thank you for the great bioinformatics workbook. I've been using the Braker tutorial as inspiration to annotate me own de novo genome and it's been quite helpful this far. I am trying to generate the transcript/EST information as part of the (required?) input for Braker2. Is the Transcript/EST information a different datatype entirely than RNA-seq, and if I don't have it then this step must be skipped? Or can it be generated from the RNA-seq data? I was thinking that if it can be generated then perhaps I'd generate a gtf file with stringtie/guided trinity, pull the fasta file from that with bedtools, and then re-align the fasta to the genome. This being said I may be way off-base and missing something obvious. If you have any advice here then that would be very valuable! Best, Dustin — Reply to this email directly, view it on GitHub <#64> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCLTPEE4I3XQ6Q42YBO5HDVAD7UZANCNFSM5Q2AWSOQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> . You are receiving this because you are subscribed to this thread. <https://github.com/notifications/beacon/ACCLTPHRUZVKV3Y73RPDGKTVAD7UZA5CNFSM5Q2AWSO2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4ROBJHZQ.gif> Message ID: ***@***.*** ***@***.***> >

[DustinSokolowski]

Hey!

Thanks so much for clearing it up!

Best,
Dustin