I am trying to perform a transcriptome assembly with Trinity for some paired-end reads (unaligned reads leftovers from a Bowtie alignment). I didn’t concatenate them previously so my input consists of 8-9 unaligned L fastas and 8-9 unaligned R fastas.
The job is still grey after a couple of hours. I know there have been issues in the past. Is it the same now or is it just a matter of time?