Question: Cufflinks analysis remains in que without running
0
gravatar for ctyoung
13 months ago by
ctyoung0
ctyoung0 wrote:

Hi Team,

Loving Galaxy! When I run my data, I use the same protocol for most all datasets. However, after running the alignment tool (usually Bowtie2 or HISAT), I am unable to get past the next analysis of using Cufflinks. I have tried it both with and without the gff file for reference annotation. Cufflinks remains in que and won't run. This has been happening for a while now. Is this expected from time to time? Also, if Cufflinks does run using the reference genome gaff file, I don't get FPKM values (when using the reference annotation gff file) but I will get an abbreviated gene symbol instead of a Cuff ID. All FPKM values show as zero. When I use Cufflinks without the reference annotation gff file, I don't get a gene symbol abbreviation, but I do get FPKM values. How can I use Galaxy tools to merge both the Cufflinks sets so that the files align both FPKM values and gene abbreviations together and match? The start/end loci should match, so that the gene symbols and FPKM values correlate to each other...

Thanks!

ADD COMMENTlink modified 13 months ago • written 13 months ago by ctyoung0

This is a known issue our team is actively working to correct. The inputs are not a factor - job dispatch had an issue. The advice is to allow queued jobs to remain queued. These will execute once the issue is resolved. More feedback after the fix, to let you and others having the same issue know what is going on.

For the data issue and reference annotation, there is probably a genome mismatch problem. Make sure that the ref genome used for alignments and the ref annotation used with tools are from the same exact genome build (compare the chromosome identifiers in the BAM datasets versus the GTF file).

Thanks! Jen, Galaxy team

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Update: The cluster fix has been made and jobs are dispatching normally. Queued jobs will execute - no need to delete/rerun. Tools that require more resources are sent to a busier cluster. That queue is expected to have some continued delays until the backlog of jobs is processed (up to a few days).

Thanks for reporting the problem and for your patience, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson23k
0
gravatar for ctyoung
13 months ago by
ctyoung0
ctyoung0 wrote:

Thank you all so much! I appreciate your attention to this issue!

ADD COMMENTlink written 13 months ago by ctyoung0
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: 89 users visited in the last hour