hisat2 library type

Question

[Bioinfonext]

Hi.....

I have a pair end strand-specific library type: fr-secondstrand so could you suggest for Hisat2 it should be --fr?

There are two option in hisat2 : --rna-strandness and --fr/--rf/--ff . please suggest which option should I mention from these two.

--rna-strandness fr

-- fr

Thanks

Answer 1

[EagleEye]

You might have to just connect these dots.

Library type info (Double check which protocol was used for sequencing):

http://onetipperday.sterding.com/2012/07/how-to-tell-which-library-type-to-use.html

HISAT2 info:

For single-end reads, use F or R. 'F' means a read corresponds to a transcript. 'R' means a read corresponds to the
 reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF. (TopHat has a similar 
option[see details below link], --library-type option, where fr-firststrand corresponds to R and RF; fr-secondstrand corresponds to F and FR.)

Tophat/cufflinks info:

http://www.nature.com/nprot/journal/v7/n3/fig_tab/nprot.2012.016_T1.html

FeatureCounts info:

Indicate if strand-specific read counting should be performed.
Acceptable values: 0 (unstranded), 1 (stranded) and 2 (reversely
stranded). 0 by default. For paired-end reads, strand
of the first read is taken as the strand of the whole fragment.
FLAG field is used to tell if a read is first or second read in a
pair.