Using TopHat2 RNA-Seq Data IOn-Torrent

[mpalegre]

Hi everyboy. I have a quick question about the "--library-type" option in the Tophat2. If the reads are from single end, RNA-seq (poly(A)) LIbrary using kit Ion Total RNA-Seq Kit v2 which options is correct. FR Unstranded? the another are -FR- First strand or FR-Second Strand. Can Anyone clarify me this?

Thanks in advance
Regards

[cmbetts]

From the manual for the kit, The Ion Adaptor Mix v2 constrains the
orientation of the RNA in the ligation reaction such that hybridization with the Ion
Adaptor Mix v2 yields template for sequencing from the 5′ end of the sense strand.

So you'd want to use the fr-secondstrand option for mapping

[mpalegre]

thanks so much

[mlou]

I found this post helpful: http://onetipperday.blogspot.co.uk/2...pe-to-use.html

Essentially I chose a few reads, BLAT to a genome and infer the library-type from the mapping result.