Question: 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?
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gravatar for bioxc
2.3 years ago by
bioxc0
bioxc0 wrote:

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!

alignment • 687 views
ADD COMMENTlink modified 2.3 years ago by Devon Ryan92k • written 2.3 years ago by bioxc0
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gravatar for Devon Ryan
2.3 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink written 2.3 years ago by Devon Ryan92k
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