Question: generating 0 bytes for trinity assembled transcript file
0
gravatar for manjumoorthy95
5 months ago by
manjumoorthy950 wrote:

I used a single end fastqsanger file ( related to the leaf of Solanum ) and tried to run trinity to get assembled transcript data, but after the program was run, i got 0 bytes generated and no transcript.fasta file was generated. why ?

single-end paired-end trinity • 168 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by manjumoorthy950

Single end input should be possible. I am running a quick test to make sure that functionality is intact at Galaxy Main.

Could you confirm that you are working at Galaxy Main https://usegalaxy.org? If not, where are you using Galaxy?

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k

Ok, I found your jobs. This might be a memory failure but will confirm that. Meanwhile, you might want to do some QA on the reads before assembly. Please do not delete the failed job(s) quite yet - they do not consume any quota space.

Galaxy tutorials, including those that cover QA/QC: https://galaxyproject.org/learn

Thanks and more feedback soon, Jen, Galaxy team

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I found the issue. It has to do with a current problem with the Get Data > EBI SRA tool. Details here: https://github.com/galaxyproject/galaxy/issues/6334

In short, reassign the datatype to be "fastqsanger.gz" for your fastq inputs. The data is compressed but is not being labeled that way -- we'll be fixing that. Follow the ticket above for updates.

How to change metadata is in the Galaxy FAQs: https://galaxyproject.org/support/

I would still recommend doing some QA on the data before attempting assembly or the tool may really run out of memory during job execution due to content issues.

And single-end Trinity jobs are confirmed to be functional at this server.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for manjumoorthy95
5 months ago by
manjumoorthy950 wrote:

So we can change the type by going to edit attributes right? So first get the data from ENA and then change its type to fastqsanger.gz and then run the trinity . Right?

ADD COMMENTlink written 5 months ago by manjumoorthy950

Yes, until the tool is fixed that will need to be done.

Or, if your accession is at NCBI, the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA can be used instead. That tool sets the metadata correctly depending on the output datatype selected on the form.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 156 users visited in the last hour