Hi, I have some Illumina data, RNA-seq, 34 bp long reads, unpaired, no strand information.
I have aligned to the reference genome using bowtie, and analysed the results using DESeq quite successfully.
I want to use cufflinks to try to find areas outside of known genes that are expressed.
Do I need to go through the SAM file and change the "strandedness" column to "*" ? Bowtie gave my data a strand value, but really this means nothing, the reads could have come from either strand, it's just the way they were sequenced as I understand.
Will this affect my cufflinks results? They talk about an XS tag with spliced alignments in the manual but I don't quite get it.
Thanks in advance