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why forward reads were much more than reverse reads In strand specific RNAseq data?

I aligned strand specific RNAseq data using tophat2 and set the parameter --fr-firststrand, After grepped forward strand by 'XS:A:+' and reverse strand by 'XS:A:-', I obtained about x4 forward reads more than reverse reads. I thought it was so strange, why forward reads were much more than reverse reads?

rna-seq
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written by yuaner • yuaner

Does your organism have 4+ more genes on the plus strand? That'd be the likely explanation.

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written by Devon Ryan Devon Ryan

Or maybe, on average, the genes on plus strand are 4x more expressed?

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written by h.mon h.mon

Sure, but what could a biological explanation for that be?

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written by Devon Ryan Devon Ryan

Thanks for your reply. I checked the number of genes on plus and minus strands, but the ratio was about 1:1. And the organism of RNAseq data was rice.

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written by yuaner • yuaner

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