Script to get the longest isoform for each 'gene'

[Jacqueline Farrell]

Hello all -- 

Before I start writing my own script I was wondering is there a script already included with Trinity that pulls out the longest isoform for each gene?  Thanks in advance for your help. 

Cheers, 

Jacqueline

[Mark Chapman]

Hi Jacqueline,

There's a python script available which would take an old trinity.fasta file, maybe you could make a few modifications to take in the newly formatted ones (i.e. TRx|...etc nomenclature):

https://github.com/jorvis/biocode/blob/master/sandbox/jorvis/filter_longest_trinity_subcomponents.py

If you get it to work feel free to post it to the group :)

Best wishes, Mark

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[Tiago Hori]

There may be another way. Trinity stats works by creating an array that contains the longest isoforms, that is how it calculates the average. 

It should be super simple to tweak that.

T.

Sent from my iPhone

[Farbod Emami]

Dear Tiago, Hi.

In which file the name of the ONLY longest Isoform per gene is stored during TrinityStats.pl running? 

On Thursday, May 21, 2015 at 7:49:27 PM UTC+4:30, Tiago Hori wrote:

There may be another way. Trinity stats works by creating an array that contains the longest isoforms, that is how it calculates the average. 

It should be super simple to tweak that.

T.

Sent from my iPhone

On May 21, 2015, at 12:02 PM, Mark Chapman <markcha...@gmail.com> wrote:

Hi Jacqueline,

There's a python script available which would take an old trinity.fasta file, maybe you could make a few modifications to take in the newly formatted ones (i.e. TRx|...etc nomenclature):

https://github.com/jorvis/biocode/blob/master/sandbox/jorvis/filter_longest_trinity_subcomponents.py

If you get it to work feel free to post it to the group :)

Best wishes, Mark

On 21 May 2015 at 15:44, Jacqueline Farrell <jacquelin...@gmail.com> wrote:

Hello all -- 

Before I start writing my own script I was wondering is there a script already included with Trinity that pulls out the longest isoform for each gene?  Thanks in advance for your help. 

Cheers, 

Jacqueline

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[Tiago Hori]

It doesn't create a file. It creates a Perl array. All I saying is that one could, if one wanted, grab that array and write a piece of code that iterates and print its contents. 

It may be easier than writing form scratch, although if the Python alternative works as is; it is easier.

<digression> 

I should really have learned Python.

</digression>

Sent from my iPhone

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[Brian Haas]

The longest transcript isn't always the 'best' transcript....  but this has been asked for so many times, I'll just write the script and post it shortly.

~b

Dear Tiago, Hi.

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------------------------------------

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[Brian Haas]

yes, we should all learn python!  ... and if I didn't have all this legacy perl code...   ;)

[Brian Haas]

Just drop the attached script into your TRINITY_HOME/util/misc folder and it should do the trick.

best,

~b

[Ken Field]

Thanks Brian! And now could you just write a script that outputs the best transcript? ;)

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[Brian Haas]

Ha!  I was thinking the same thing when I put this together.  It would be doable, but not something that would be done in just a few minutes...   It would involve the Trinotate report and the RSEM expression matrix.

I'm also curious about what the utility would be for it, as I try to make the claim that you simply don't have to do these things:

http://trinityrnaseq.github.io/trinity_faq.html#ques_why_so_many_transcripts

I'm clearly biased...

~b

[Tiago Hori]

Isn't that called magic?

Sent from my iPhone

[Farbod Emami]

Dear Brian, Hi, 

I have used your script for longest isoformes as follow :

get_the_longest_. . .  Trinity.fasta > longest_trinity_isoforms.fasta

but it seems that the out put isoformes (transcripts) are not according to transcripts order in the main file, yes?

I mean it is not as :

Transcript No. 1 Longest isoform

Transcript No. 2 Longest isoform

Transcript No. 3 Longest isoform

and so on.

(of course i think it should not be any problem with it!)

Thank you

On Friday, May 22, 2015 at 3:00:50 AM UTC+4:30, Tiago Hori wrote:

Isn't that called magic?

Sent from my iPhone

On May 21, 2015, at 6:41 PM, Ken Field <kfi...@bucknell.edu> wrote:

Thanks Brian! And now could you just write a script that outputs the best transcript? ;)

On Thu, May 21, 2015 at 2:47 PM, Brian Haas <bh...@broadinstitute.org> wrote:

Just drop the attached script into your TRINITY_HOME/util/misc folder and it should do the trick.

best,

~b

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[Brian Haas]

that's right, they don't retain their original order in the Trinity.fasta file.  Sequences are sorted according to length (descendingly) just for aesthetics.

~b

On Sat, May 23, 2015 at 12:13 AM, Farbod Emami <farbo...@gmail.com> wrote:

Dear Brian, Hi, 

I have used your script for longest isoformes as follow :

get_the_longest_. . .  Trinity.fasta > longest_trinity_isoforms.fasta

but it seems that the out put isoformes (transcripts) are not according to transcripts order in the main file, yes?

I mean it is not as :

Transcript No. 1 Longest isoform

Transcript No. 2 Longest isoform

Transcript No. 3 Longest isoform

and so on.

(of course i think it should not be any problem with it!)

Thank you

On Friday, May 22, 2015 at 3:00:50 AM UTC+4:30, Tiago Hori wrote:

Isn't that called magic?

Sent from my iPhone

On May 21, 2015, at 6:41 PM, Ken Field <kfi...@bucknell.edu> wrote:

Thanks Brian! And now could you just write a script that outputs the best transcript? ;)

On Thu, May 21, 2015 at 2:47 PM, Brian Haas <bh...@broadinstitute.org> wrote:

Just drop the attached script into your TRINITY_HOME/util/misc folder and it should do the trick.

best,

~b

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[Joseph Lee]

This works fine and REALLY helps me a lot!!!

I have been seeking a tool like this since i fail to write a script doing this work!

thx you, Brian!!!

JLee

Brian Haas於 2015年5月23日星期六 UTC+8下午9時48分32秒寫道：

Dear Brian, Hi, 

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[Farbod Emami]

Dear Brian, Hi.

I have used your script for collecting longest Isoform per gene. I was thinking that it must be only one transcripts for each gene (some people call it unigene) after running the scripts, but when I was using TransRate program (http://hibberdlab.com/transrate/getting_started.html) to check my assembly  contigs, I accidentally realized that there are several cases that begins with the similar beginning in the name. please check this sample:

$ cat '/home/emami/Soft2/trinityrnaseq-2.0.6/util/misc/Farbod_longest_isoform.fasta'  | grep TR85783
>TR85783|c0_g2_i1 len=6498 path=[12981:0-2513 12982:2514-2543 12983:2544-6497] [-1, 12981, 12982, 12983, -2]
>TR85783|c0_g1_i1 len=6498 path=[12984:0-2513 12985:2514-2543 12986:2544-6497] [-1, 12984, 12985, 12986, -2]
>TR85783|c1_g1_i1 len=923 path=[1801:0-847 1802:848-922] [-1, 1801, 1802, -2]

is it normal or there is some error in the script?

Thank you

Farbod

Dear Brian, Hi, 

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[Mark Chapman]

Hi Farbod,

The same TR number doesnt mean the same component ('gene'). Its just the last number that differs between transcripts.

eg 

>TR85783|c0_g2_i1

>TR85783|c1_g1_i1

are different components ('genes')

>TR85783|c0_g2_i1

>TR85783|c0_g2_i2

are the same component ('gene')

Although in your example the first two components, although supposedly different, look the same according to the 'path'. Maybe something odd has happened here (Brian?). But the script to isolate one isoform per gene is working right, as per your question to the group.

Best wishes, Mark

Dear Brian, Hi, 

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[Cera Fisher]

Thanks for writing the script even though you didn't think we should use it. :) In my case, I've got the transcriptomes of two non-model organisms and I'm really just trying to find orthologs between the two in order to do some cross-species gene expression analysis, which I'm doing by reciprocal blast. It seemed like it would reduce complication if I only had one transcript from each gene, and it seemed simplest to choose the longest transcript for each Trinity component. I'll let you know how this goes. 

Sincerely,

a naive grad student

On Thursday, May 21, 2015 at 5:44:59 PM UTC-4, Brian Haas wrote:

Ha!  I was thinking the same thing when I put this together.  It would be doable, but not something that would be done in just a few minutes...   It would involve the Trinotate report and the RSEM expression matrix.

I'm also curious about what the utility would be for it, as I try to make the claim that you simply don't have to do these things:

http://trinityrnaseq.github.io/trinity_faq.html#ques_why_so_many_transcripts

I'm clearly biased...

~b

On Thu, May 21, 2015 at 5:41 PM, Ken Field <kfi...@bucknell.edu> wrote:

Thanks Brian! And now could you just write a script that outputs the best transcript? ;)

On Thu, May 21, 2015 at 2:47 PM, Brian Haas <bh...@broadinstitute.org> wrote:

Just drop the attached script into your TRINITY_HOME/util/misc folder and it should do the trick.

best,

~b

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