Can I use strand-specific RNA-seq data as non-stranded data when aligning them by some software (e.g. tophat, using fr-unstranded) if I just want to calculate the gene expression level?

Question

[bioxc]

Can I use strand-specific RNA-seq data as non-stranded data when aligning them by some software (e.g. tophat, using fr-unstranded) if I just want to calculate the gene expression level? If so, how does it affect the result except for losing the strand information, e.g. the gene expression calculation? Thanks!

Answer 1

[Devon Ryan]

Can you do that? Yes, but there's no reason to want to do so. You're just going to increase your multimapper rate and decrease the amount of data you're going to get out of the process.