Which ORF to consider among different isoforms?

[ConcettaDe4]

Hi! I have assembled my transcripts with Trinity using stranded RNA-seq data and after I predicted ORF with Transdecoder. After TransDecoder.Predict I noticed that for some transcripts I have more than one ORF prediction, such as in the below example:

Transcript.p2 ORF type:complete len:142 (+),score=22.85 Transcript:588-1013(+)
Transcript.p1 ORF type:5prime_partial len:185 (-),score=23.89 Transcript:1076-1630(-)
Transcript.p3 ORF type:5prime_partial len:138 (+),score=14.89 Transcript:1-414(+) 

I usually selected the p1 ORF but I noticed that often the complete ORF is not the p1. So, I was wondering which ORF I should select.

Thank you,

Concetta

[brianjohnhaas]

Hi Concetta,

With the predict step, there's an option: --single_best_only

On Thu, Feb 10, 2022 at 11:28 AM ConcettaDe4 @.***> wrote:

Hi! I have assembled my transcripts with Trinity using stranded RNA-seq data and after I predicted ORF with Transdecoder. After TransDecoder.Predict I noticed that for some transcripts I have more than one ORF prediction, such as in the below example:

Transcript.p2 ORF type:complete len:142 (+),score=22.85 Transcript:588-1013(+) Transcript.p1 ORF type:5prime_partial len:185 (-),score=23.89 Transcript:1076-1630(-) Transcript.p3 ORF type:5prime_partial len:138 (+),score=14.89 Transcript:1-414(+)

I usually selected the p1 ORF but I noticed that often the complete ORF is not the p1. So, I was wondering which ORF I should select.

Thank you,

Concetta

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[ConcettaDe4]

OK thank you!

[ConcettaDe4]

Hi!

I have an additional question. I have assembled my transcripts with rnaSPAdes using RNA-seq produced with Illumina stranded protocol.

I would like to know if I should also include the parameter -S during the prediction considering how my RNA-seq libraries have been produced.

Thank you,

Concetta

[brianjohnhaas]

Yes, that would make sense, assuming all assembled transcripts are in their 'sense' orientation.

best,

~b

On Fri, Feb 18, 2022 at 11:21 AM ConcettaDe4 @.***> wrote:

Hi!

I have an additional question. I have assembled my transcripts with rnaSPAdes using RNA-seq produced with Illumina stranded protocol.

I would like to know if I should also include the parameter -S during the prediction considering how my RNA-seq libraries have been produced.

Thank you,

Concetta

— Reply to this email directly, view it on GitHub https://github.com/TransDecoder/TransDecoder/issues/144#issuecomment-1044782869, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXYOIT5VCGJRZ4WGDXLU3ZWYRANCNFSM5OBI43KA . 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.

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas