I am trying to align paired end read data to the zebrafish transcriptome and for each sample I encounter the following error in the tophat_reports step:
Error: singleton getQRead() failed for id# 1627678
(id# differs for each sample)
The command I used was:
/usr/bin/tophat --library-type fr-firststrand -p 8 -N 2 -o ../tophat_alignments/SRR372798 -G ../annotations/Danio_rerio.Zv9.75.gtf Zv9 SRR372798_1_val_1.fq SRR372798_2_val_2.fq
I can't seem to find any other reports of this error.
Does anyone have any idea what might be causing this?