I tested two different options while running HTSeq-Count,
-s no and
-s reverse. This are the results:
For the option
-s reverse there are lower ambiguous values but higher no_feature than for
As far as I know this option depends on the construction of the library, but when they gave me this sequences they didn't mention it. All I know is that it's was constructed under a Illumina protocol and that it was a Paired-End experiment of RNA-Seq from peach (Prunus persica).
I'm inclined to think that less ambiguous values are just better, even than with more no_feature values.
So, which one it's right?
This are the results from