Is Star Managing Strand-Specific Data ?

Question

[Nicolas Rosewick]

Hi,

I've strand-specific data and I checked in the STAR manual but there is nothing about strand-specific data. So is STAR managing strand-specific data (paired-end) ?

Thanks,

N.

Answer 1

[Johan]

I checked the STAR 2.2 manual available here: ftp://ftp2.cshl.edu/gingeraslab/tracks/STARrelease/2.2.0/STARmanual_2.2.0.pdf. And it states the following about strand specific data:

If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will need to use --outSAMstrandField intronMotif option, which will generate the XS strand attribute for all alignments that contain splice junctions. The spliced alignments that have undefined strand (i.e. containing only non-canonical junctions) will be suppressed.

If you have stranded RNA-seq data, this option is not required – instead, you need to use the correct library option --library-type options for Cufflinks runs. For example, --library-type fr-firststrand should be used for the “standard” dUTP protocol.

So in my understanding if you have strand specific data you don't need to do anything special in the alignment step, but use the library-type option in Cufflinks to indicate the correct strandedness.