Is Star Managing Strand-Specific Data ?
1
2
Entering edit mode
11.8 years ago

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.

strand rna-seq • 12k views
ADD COMMENT
6
Entering edit mode
11.8 years ago
Johan ▴ 890

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1408 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6