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!