Add Strand tag to hisat2 alignments

Question

[GR]

Hi All,

Hisat2 does not report XS tag for each alignment like tophat2. How do I extract Strand info and add XS tag for each alignment?

RT

[GenoMax]

Option seems to run your alignments with --dta option (see: A: Adding tag XS to HISAT2 sam files perior to StringTie )

[GR]

Thanks for your response. I think --dta adds XS tag only for reads spliced reads alignments. I need this XS tag for all the reads.

Answer 1

[Istvan Albert]

You will need to use the --rna-strandness parameter:

--rna-strandness <string>

Specify strand-specific information: the default is unstranded.

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. With this option being used, every read alignment will have an XS attribute tag:

’+’ means a read belongs to a transcript on ‘+’ strand of genome. ‘-‘ means a read belongs to a transcript on ‘-‘ strand of genome.

(TopHat has a similar option, –library-type option, where fr-firststrand corresponds to R and RF; fr-secondstrand corresponds to F and FR.)

this info can be found in the manual:

http://daehwankimlab.github.io/hisat2/manual/