Question: Query for inputting Hisat2 BAM with dataset collections for Stringtie analysis
gravatar for pravikumar
6 months ago by
pravikumar0 wrote:

Hi, I have data set collections ( 3 biological replicates) that I could run on HiSAT2 and I have BAM files with dataset collection. I have tried multiple times with Stringtie and even with Cufflinks but my analysis files are always lined up for analysis and it never gets through. I do not get any error message either. With my last query I was asked to recheck the HiSAT input files as well, I have done that and it does not show any error. Any suggestions for me to move forward.


stringtie job rna-seq hisat2 quota • 259 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by pravikumar0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


It looks like your Stringtie jobs completed, as well as some Cufflinks jobs. The Cuffdiff jobs are still queued (started up earlier today).

Your analysis does have a problem unrelated to the cluster queue. Specifically, the options for HISAT2 need to be set differently when the result is input to Cufflinks versus Stringtie. It looks like this reporting option was not set when creating HISAT2 BAMs input to Cufflinks. I didn't check the Stringtie input HISAT2 BAMs, but you should. If both are not corrected, the results from downstream tools will not be scientifically valid, or the jobs will fail (error). You'll need to rerun HISAT2 with the proper settings, then rerun the downstream tools.

Galaxy tutorials, including those for RNA-seq:

Tutorials using Galaxy Main

These work at Galaxy Main and often at other public Galaxies.

Galaxy Training Network

GTN network tutorial's tools will work at various public Galaxy servers. Find out which public server(s) support any particular tutorial under "Galaxy instances". Some will also have a pre-configured Galaxy Docker available and this is noted on the tutorial group's landing page.

  • RNA-seq tutorials are under the group >> Transcriptomics

More about jobs:

Jobs are run in the order submitted, are added to a master queue (all users), then execute. Concurrency quotas are in place to help ensure equal access for everyone, whether running individual jobs or batch jobs.

Important: Unless you detect an input/setting problem and need to rerun to correct those, queued jobs should be left queued. When jobs are deleted/rerun, the new jobs are added back at the end of the queue, extending wait time. Permanently delete any jobs queued that you no longer wish to run or have already used to start a rerun. This clears them from the server quicker. Note that jobs that are already executing (yellow) will take longer to clear/free up job concurrency quotas.


Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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