Locally cached sequence not detected from DBkey in cuffmerge when using mm10

Question: Locally cached sequence not detected from DBkey in cuffmerge when using mm10

3.5 years ago by

Canada

max.shafer • 30 wrote:

Hi,

I'm running a cufflinks pipeline on the public server, and I'm having trouble using the locally cached sequence as a reference when building my cuffmerge file of cufflinks assembled transcripts for further cuffdiff analysis.

When I set up the job with my cufflinks outputs (produced either with or without using sequence and/or annotation information) Galaxy gives me "no options available" for the locally cached sequence (it actually does briefly flash mm10 before ultimately deciding there are no options). All my files in my history have the correct dbkey ("mm10"). I have the same problem with cuffcompare.

It can detect and find the right locally cached sequence when running cufflinks or cuffquant though.

Thanks for any help,

Max

cuffmerge cufflinks dbkey cuffdiff • 1.9k views

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modified 3.4 years ago by cookseq2 • 0 • written 3.5 years ago by max.shafer • 30

3.5 years ago by

Yiwei Ai • 20

United States

Yiwei Ai • 20 wrote:

I also have the same problem. Waiting for updates. Thanks

ADD COMMENT • link written 3.5 years ago by Yiwei Ai • 20

3.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am able to reproduce this. We are investigating and will get back when resolved. Thanks for reporting the issue!

Jen, Galaxy team

ADD COMMENT • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

I'm having the same problem as Max. I'm not sure if it has been resolved yet but it's not working for me. I'm trying to use the built in mm10 reference genome as my sequence data in Cuffmerge (also to then do differential analysis with Cuffdiff), but nothing is showing up in "locally cached". I assume "locally cached" should bring up all the built in genomes? I.e. the same one I used in TopHat to map my reads.

If this does not work, what parameters can I use in the UCSC Main table browser to download the correct FASTA file for this application? I'm not sure I understand all the track options there, but is it possible to download the same sequence data from there?

Thanks

ADD REPLY • link written 3.5 years ago by nashedm • 10

Is there an update on this situation? I'm still having the same problem.

ADD REPLY • link written 3.5 years ago by max.shafer • 30

I'm still having the same problem as well. 2 days ago I think it worked briefly- I was able to choose "locally cached" but there was no drop-down menu to select a genome. I assumed maybe it just automatically detects the appropriate genome based on the cufflinks files or something- I'm not sure. But it allowed me to choose the "locally cached" option, execute, and produced a merged file. I was able to do this once, but since then, it's back to the same problem where a drop-down menu appears under "locally cached", briefly shows mm10, then shows "no options available".

ADD REPLY • link written 3.5 years ago by nashedm • 10

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello all,

First, thank you for reporting the issue. As replied earlier, we were able to confirm the problem. The resolution is still in progress. To track the work done, please follow this Github issue: https://github.com/galaxyproject/galaxy/issues/388

Thank you for your patience, Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.4 years ago by

cookseq2 • 0

United Kingdom

cookseq2 • 0 wrote:

Can you use a FASTA reference file instead of the locally cached sequence data, as unfortunately the locally cached sequence data is still unavailable.

Richard Hogg

ADD COMMENT • link written 3.4 years ago by cookseq2 • 0

3.4 years ago by

cookseq2 • 0

United Kingdom

cookseq2 • 0 wrote:

The only workaround i have found for this problem involves clicking on the 'rerun job again' button on a CuffDiff run in which the sequence data could be found. Though i did this for hg19 i don't think there would be any difference if you needed to use mm10. I hope this helps.

ADD COMMENT • link written 3.4 years ago by cookseq2 • 0

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