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!
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!
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.