Question about TransDecoder.Predict output format

[John Martin]

I have a set of translations from TransDecoder.Predict and it seems to have applied an additional suffix to the input transcript names. Eg. TRINITY_DN10195_c0_g1_i9  became TRINITY_DN10195_c0_g1_i9.p1.   And in some cases a single isoform will have > 1 versions with different .p# suffixes.   I was unable to find anything about this in the wiki, can someone tell me what this suffix indicates?   I think its probably multiple translations for a single isoform but I want to be sure.  

Thanks,

John

[Brian Haas]

Hi John,

The different p's represent different potential coding regions (orfs) that were found on the corresponding transcript sequence.

best,

~b

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[John Martin]

Thanks!

On Wednesday, April 10, 2019 at 3:14:28 PM UTC-5, Brian Haas wrote:

Hi John,

The different p's represent different potential coding regions (orfs) that were found on the corresponding transcript sequence.

best,

~b

On Wed, Apr 10, 2019 at 3:28 PM John Martin <jmarti...@gmail.com> wrote:

I have a set of translations from TransDecoder.Predict and it seems to have applied an additional suffix to the input transcript names. Eg. TRINITY_DN10195_c0_g1_i9  became TRINITY_DN10195_c0_g1_i9.p1.   And in some cases a single isoform will have > 1 versions with different .p# suffixes.   I was unable to find anything about this in the wiki, can someone tell me what this suffix indicates?   I think its probably multiple translations for a single isoform but I want to be sure.  

Thanks,

John

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[Bioinform]

I am bit confused with the output. Which sequence to use for further downstream analysis.

If i look into the header and sequence i see different patterns and different number.

transcript/10491.p2  ORF type:complete len:422
transcript/10491.p1  ORF type:5prime_partial len:1164 (5prime_partial is larger in size)
 
transcript/77900.p2  ORF type:complete len:168
transcript/77900.p1  ORF type:complete len:735 - both complete one large and other small

transcript/109033.p1  ORF type:complete len:524 - complete is larger in size
transcript/109033.p2  ORF type:5prime_partial len:105

transcript/19731.p1  ORF type:complete len:233 (missing p2)
transcript/19731.p3  ORF type:complete len:110
transcript/19731.p4  ORF type:complete len:106

transcript/91372.p1  ORF type:complete len:207 (- bigger in size)
transcript/91372.p2  ORF type:5prime_partial len:198
transcript/91372.p3  ORF type:complete len:116

transcript/59793.p1  ORF type:complete len:185 - around similar size
transcript/59793.p2  ORF type:complete len:160
transcript/59793.p3  ORF type:complete len:150
transcript/59793.p4  ORF type:complete len:118

transcript/20937.p1  ORF type:complete len:712 (missing p2, p3, p4)
transcript/20937.p5  ORF type:complete len:100

Which one should i select here. Is there way i can extract the largest one?

Best

[Brian Haas]

Hi,

In Transdecoder.Predict, there should be a parameter to select just the single 'best' one if that's what you're after.

To view this discussion on the web visit https://groups.google.com/d/msgid/transdecoder-users/0a7bf00d-a128-4dc8-b28f-9fb7132aaf78n%40googlegroups.com.