Strandness option disappeared in Bowtie2


I ran Bowtie2 today and I couldn’t find the strand-specificity option. Is there a new update? I doubt I missed it, it was under “Paired-end option” as I remember. I don’t know what to choose for featureCounts now :frowning:


Hi @Sammy,
I have checked the previous versions of Bowtie2 but I couldn’t find any significant change regarding the strand-specificity option. I suggest you to use HISAT2, since it provides this option.


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