Hello.
I am still researching this issue
but essentially I am mapping cut adapt trims for Rnaseq data and when I trim them according to the manual and align them as single end reads with lib type -unstranded I get the map percent as 91%
however if I align them as lib type first strand, or lib type second strand using tophat2 I get the map percent as 4%.
what is the cause of this? I do have my qc reports.
I am still researching this issue
but essentially I am mapping cut adapt trims for Rnaseq data and when I trim them according to the manual and align them as single end reads with lib type -unstranded I get the map percent as 91%
however if I align them as lib type first strand, or lib type second strand using tophat2 I get the map percent as 4%.
what is the cause of this? I do have my qc reports.
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