Older Versions: transcripts_to_best_scoring_ORFs.pl

[taua...@gmail.com]

Hi all!

I am starting analyses of transcriptomes and following from a pipeline used previously in my lab. But I noticed that it had an older version o TransDecoder with the script transcripts_to_best_scoring_ORFs.pl and the file saved at the end was best_candidates.eclipsed_orfs_removed.pep (contains peptide sequences for the final candidate ORFs; shorter candidates with longer ORFs were removed).

I want to use the most recent version of the program, but I am not absolutely sure which is the recent version of that program. Does anybody know which new program correspond to old ones?

Thank you!

[Brian Haas]

Hi

You can download the latest version of transdecoder from the website

http://Transdecoder.github.io

-Brian

(by iPhone)

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[Tauana Junqueira da Cunha]

Oh Thank you, Brian.

But I think I didn't express myself correctly in the first email. I did download the latest version, but the names of the scripts/commands are not the same as in old versions, and I would like to know which scripts from the new version correspond to the -best-scoring-ORFs from the old version.

Does this make sense?

Thanks!

[Brian Haas]

Oh, I see!   It's all pretty much the same as the earlier version, but refactored and split into the two discrete steps instead of a single step, in order to provide more flexibility with including pfam and blast results as part of the ORF selection process.

I'd recommend just sticking with the new version and go through the web documentation to see how the current workflow is organized.

best,

~brian

On Fri, Aug 19, 2016 at 8:50 AM, Tauana Junqueira da Cunha <taua...@gmail.com> wrote:

Oh Thank you, Brian.

But I think I didn't express myself correctly in the first email. I did download the latest version, but the names of the scripts/commands are not the same as in old versions, and I would like to know which scripts from the new version correspond to the -best-scoring-ORFs from the old version.

Does this make sense?

Thanks!

On Aug 19, 2016, at 08:02, Brian Haas <bh...@broadinstitute.org> wrote:

Hi

You can download the latest version of transdecoder from the website

http://Transdecoder.github.io

-Brian

(by iPhone)

On Aug 18, 2016, at 6:11 PM, taua...@gmail.com wrote:

Hi all!

I am starting analyses of transcriptomes and following from a pipeline used previously in my lab. But I noticed that it had an older version o TransDecoder with the script transcripts_to_best_scoring_ORFs.pl and the file saved at the end was best_candidates.eclipsed_orfs_removed.pep (contains peptide sequences for the final candidate ORFs; shorter candidates with longer ORFs were removed).

I want to use the most recent version of the program, but I am not absolutely sure which is the recent version of that program. Does anybody know which new program correspond to old ones?

Thank you!

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[taua...@gmail.com]

Thanks, Brian!

If I understood correctly from the webpage, I am interested in running TransDecoder.LongOrfs and TransDecoder.Predict after.

Do you know where I can find information on the flags/arguments that are available? I tried -help/-h but get nothing. Also didn't find it in the github page. It was not clear to me if the Predict uses output from the LongOrfs, or even what the output is for the first step.

Thank you for all the help.

Tauana

On Friday, August 19, 2016 at 9:20:08 AM UTC-4, Brian Haas wrote:

Oh, I see!   It's all pretty much the same as the earlier version, but refactored and split into the two discrete steps instead of a single step, in order to provide more flexibility with including pfam and blast results as part of the ORF selection process.

I'd recommend just sticking with the new version and go through the web documentation to see how the current workflow is organized.

best,

~brian

On Fri, Aug 19, 2016 at 8:50 AM, Tauana Junqueira da Cunha <taua...@gmail.com> wrote:

Oh Thank you, Brian.

But I think I didn't express myself correctly in the first email. I did download the latest version, but the names of the scripts/commands are not the same as in old versions, and I would like to know which scripts from the new version correspond to the -best-scoring-ORFs from the old version.

Does this make sense?

Thanks!

On Aug 19, 2016, at 08:02, Brian Haas <bh...@broadinstitute.org> wrote:

Hi

You can download the latest version of transdecoder from the website

http://Transdecoder.github.io

-Brian

(by iPhone)

On Aug 18, 2016, at 6:11 PM, taua...@gmail.com wrote:

Hi all!

I am starting analyses of transcriptomes and following from a pipeline used previously in my lab. But I noticed that it had an older version o TransDecoder with the script transcripts_to_best_scoring_ORFs.pl and the file saved at the end was best_candidates.eclipsed_orfs_removed.pep (contains peptide sequences for the final candidate ORFs; shorter candidates with longer ORFs were removed).

I want to use the most recent version of the program, but I am not absolutely sure which is the recent version of that program. Does anybody know which new program correspond to old ones?

Thank you!

--

[Brian Haas]

Hi

If you run either script with no parameters or with -h, it should give the full usage info.  Instructions are also provided on the project website.  If the script doesn't run 'out of the box', it could be a permissions issue. Try

   chmod 775 scriptname

and then try running it.

Or you could run

   perl scriptname 

to execute it, but that's not ideal.

Best,

-Brian

(by iPhone)

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[taua...@gmail.com]

Thanks Brian,

I was doing something wrong, but I can see the -help now and it is running!

Last thing, does it support parallelization? I was running it in three cpus, but I am not even sure it's using them.

Thanks!

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[Brian Haas]

Only the cd-hit process will end up using the multiple threads.  The rest is not multithreaded as of yet.

best,

~b

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[taua...@gmail.com]

Dear Brian,

After running isoform selection, I noticed the script we have been using in the lab was made for older versions of Trinity that had a different header structure (component). I am updating my script to work with the newest Trinity, but I just wanted to check that TransDecoder is also compatible with that (consider DN[0-9]_c[0-9] as a component, instead of just the c[0-9]).

Also, I noticed in the help page that there is an option for selection of the longest ORF. Using this flag completely replaces the final output (.pep) file with only the single best ORF or does it save an additional file with the best ORFs?

Thank you!

Tauana

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[Brian Haas]

Hi Tauana,

Responses below

On Thu, Aug 25, 2016 at 3:51 PM, <taua...@gmail.com> wrote:

Dear Brian,

After running isoform selection, I noticed the script we have been using in the lab was made for older versions of Trinity that had a different header structure (component). I am updating my script to work with the newest Trinity, but I just wanted to check that TransDecoder is also compatible with that (consider DN[0-9]_c[0-9] as a component, instead of just the c[0-9]).

TransDecoder should be compatible with any target transcriptome file. You need to provide the 

    --gene_trans_map   file

that provides the gene-to-trans relationship.  Trinity has a utility to provide this based on your fasta file:

      trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl  Trinity.fasta > gene_trans_map.txt

 

Also, I noticed in the help page that there is an option for selection of the longest ORF. Using this flag completely replaces the final output (.pep) file with only the single best ORF or does it save an additional file with the best ORFs?

It should give you a single pep file having just the longest ORF per transcript.

 

Thank you!

Tauana

[taua...@gmail.com]

Thank you Brian, I was able to use both options.

Looking at the result of the single_best_orf, I realized it is the longest ORF per transcript, but not per gene, correct? It does not seem to be equivalent to isoform selection because I still get multiple isoforms per gene.

[Brian Haas]

Yes, that's right. ;-)     I guess multiple transcripts per gene X multiple peptides per transcript can be a bit much.

If you want, you can try:

   trinityrnaseq/util/misc/get_longest_isoform_seq_per_trinity_gene.pl

to first pull the single longest isoform transcript sequence per trinity gene, and then use TransDecoder with the longest orf only option.

I'm sure there's a better way to get what you want, but it's not trivial to select the 'best' of everything by only length criteria, and I don't have another canned solution for it at the moment.  Operationally, though, I think it'll do what you want.

best,

~brian

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