Question: Bowtie trouble for aligning small RNA reads
gravatar for SRpara
4.2 years ago by
European Union
SRpara10 wrote:

Hi there,

I’ve been trying to use Bowtie to align my small RNA NGS reads (fastq groomed, for Sanger Illumina 1.8+ in ASCII) with a builtin genome. I have tried both using Bowtie2 and the Map Illumina with Bowtie options but neither run in the history will go beyond the grey colouring i.e. They continuously say “waiting to run”. I’ve tried using the default settings and have played around with the settings just to see if that helps but have had no luck. I assume it must be a problem with the fastqsanger file of reads. Can you advise me as how to resolve this problem?

Many thanks for your help in advance!

bowtie • 1.9k views
ADD COMMENTlink modified 4.2 years ago by Nate Coraor3.2k • written 4.2 years ago by SRpara10

From looking on BioStar I see other people have queried this too and the response seems to be just wait as this can take time. I have been waiting for over a day in some cases. Is that normal ok? I will give them longer and will ensure not to restart the runs. Is it a case of it it isn't going to work then eventually I should see the red colouring for the dataset? Also, I have ran a few other things (clips on other samples)  in the meantime and they have jumped the queue and completed without problems. Is that ok to expect? Can running other jobs hold back the Bowtie job?


Many thanks for your time. I look forward to any suggestions!

ADD REPLYlink written 4.2 years ago by SRpara10

Be aware that mature tRNAs get extended with CCA and some also get spliced. If you align your reads back to a built-in genome you will probably not align all reads derived from tRNAs.

ADD REPLYlink written 4.2 years ago by y.hoogstrate460
gravatar for Nate Coraor
4.2 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:


Unfortunately wait times in the 1-2 day range have become pretty common. We're working on reducing the load on our dedicated cluster for mapping jobs. One new feature currently in beta is the ability to schedule jobs on TACC's Stampede supercomputer. You can select it from the Job Resource Parameters selector at the bottom of the Bowtie tool form. Wait times here vary but are generally shorter. Please give it a try and let us know if you run in to problems.

You may also find the test/development queues useful to test tool parameters on small data before submitting to the regular queues.

More details on the job resource selections.



ADD COMMENTlink written 4.2 years ago by Nate Coraor3.2k

Thanks very much for your help Nate!

ADD REPLYlink written 4.2 years ago by SRpara10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour