Question: Salmon not working
0
gravatar for m_ko
10 months ago by
m_ko10
m_ko10 wrote:

I have not been able to get Salmon to work for the past four days. Following the instructions of a previous post, I deleted the old jobs and I have been starting new ones for the past few days but they remain on queue and do not progress.

rna-seq • 298 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by m_ko10

Was the tool working for you before?are you using usegalaxy.org?

ADD REPLYlink modified 10 months ago • written 10 months ago by Guy Reeves1.0k

I just tried the tool on use galaxy.org just now with the test datasets given on the program homepage salmon.It worked fine for me. Finished in a few seconds and output looks good.

Here is the history I have shared it publicly and through the link https://usegalaxy.org/u/guy1/h/salmon-test-dataset

I think you may need to look into the possibility that there is something wrong with your files or they are too large.

Try running the test yourself Cheers

Guy Ps I may have been better if you responded to my question as a 'comment' and not as a 'reply' as doing this makes it look like your issue has been resolved when I do not think it yet has. Maybe you can delete your reply and put if in as a comment - if that is possible. This maximises your chances of getting help.

ADD REPLYlink written 10 months ago by Guy Reeves1.0k
0
gravatar for m_ko
10 months ago by
m_ko10
m_ko10 wrote:

Yes, it worked fine before. The job would be completed in a few hours.

ADD COMMENTlink written 10 months ago by m_ko10
1

Yes, I tried it with the test dataset and as you mentioned, it worked fine in a few minutes with the same results. I do think the problem is that my files are too large. The reference transcriptome is Xenopus (2.6GB) and my transcriptome from Trinity is 295.9 MB. Is there a different route that is recommended to quantify the transcriptome from Trinity?

ADD REPLYlink written 10 months ago by m_ko10

To test if it is the file size try spliting the ref into two and see if that helps. But my recollection is if you exceed the memory allocated to the tool the dataset should go red, not just stay grey. If you need instructions on how to split the ref file I can help

ADD REPLYlink written 10 months ago by Guy Reeves1.0k

Yes, how do I go about splitting the file into two? Thank you.

ADD REPLYlink written 10 months ago by m_ko10

1run 'FASTA-to-Tabular' on the ref file.

2 use 'Select first ' on the output to select as many sequences as you want in the file

3 on this output run 'Tabular-to-FASTA '

This should give you a smaller file.

If you want to select lines not starting at the beginning of the file you can use a sequential combination of 'Select last', 'Select first ' and 'Remove beginning ' the following tools at step 2 (not in any particular order here )

ADD REPLYlink modified 10 months ago • written 10 months ago by Guy Reeves1.0k
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