Half sense and half anti-sense

Question

[zizigolu]

Hello

I have small RNAseq from plasma but it seems strange to me that I get so many "antisense" hits for both RefSeq and lncRNAs. I searched and people say ***there might be something wrong with the way in which the reads are processed (presumably doing RT and amplification, so I actually lose the strandedness information?)***. Read prosecuting from QC, alignment, raw read quantificatio n has been done by a company

So what can I do know? I have access to the fastq files

Should I do the alignment again? I don't in which step something has gone wrong though

Any help please

[GenoMax]

Find out which kit was used for the prep. And then check the manual to understand which strand was actually captured.