I am running htseq-count for a RNA-seq and I got this error:
Fatal error: Unknown error occured [bam_sort_core] merging from 28 files... Error occured when processing GFF file (line 1 of file /galaxy-repl/main/files/020/688/dataset_20688618.dat): Feature TRINITY_DN17_c0_g1_i1 at TRINITY_DN17_c0_g1_i1:[0,272)/. does not have strand information but you are running htseq-count in stranded mode. Use '--stranded=no'. [Exception type: ValueError, raised in count.py:57]
Apparently, my data is not from a strand-specific assay , but the data was obtained with Illumina Truseq Stranded mRNA library PrepKit. I have understood that for this protocol, the library type in TopHat should be fr-firststrand and in htseq-count I should select "reverse" in the strand option. However, I am getting this error. Should I use the unstranded mode instead? I am very new to RNA-Seq and I would highly appreciate your help.