I am working with Single End cDNA transcriptomic data and it has been determined by Salmon using the auto detect method evoked by the -l A or --libType A options that the raw reads are unstranded.
My question is whether or not it is possible to know the strandedness from unstranded single end reads.
It seems like it is impossible unless Single End sequencing may provide some directionality information of some sort.
Any help would be great. Thank you
1 answer
I think you're mixing up concepts here. Strandedness means from which strand a gene is transcribed. If a protocol is unstranded then the information is lost. Sequencing on the other hand always has a directionality because DNA is directional (5'->3') and PCR as such is directional as well, but the two concepts have nothing in common. Unstranded protocols are unstranded, that's it.
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