Question: Strand Specificity
gravatar for Aleks Schein
6.6 years ago by
Aleks Schein60
Aleks Schein60 wrote:
Dear All, I am trying to analyze my RNAseq data by TopHat-Cufflinks package based on Galaxy. I used Epicentre ScriptSeq strand-specific library construction protocol, which I assume, produces a second-strand library. When I set FR option to "second strand" and run TopHat and Cufflinks it results in confusing transcript orientation. Cufflinks-assembled transcript with multiple exons are oriented as expected. However, transcripts that entirely reside in one exon/intron or intergenic region are labeled in an opposite way. If TopHat accepted hits track contains negative-strand reads (colored red), transcript is labeled as "positive" and vice versa. An example is shown in the attached screenshot. Both transcripts TCONS_00000014 and TCONS_00000015 were mapped to "+" strand, though reads that represent them had been mapped to "-" strand. Is there a way to solve this issue? Regards, Aleks Schein
rna-seq cufflinks • 1.0k views
ADD COMMENTlink modified 6.6 years ago by Jeremy Goecks2.2k • written 6.6 years ago by Aleks Schein60
gravatar for Jeremy Goecks
6.6 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Aleks, This an assumption probably worth verifying before going further. The Tophat documentation may be helpful as well: I haven't heard of or encountered this problem before. Your best bet is probably to email the Tophat/Cufflinks authors and see if they can shed light on your issues: Good luck, J.
ADD COMMENTlink written 6.6 years ago by Jeremy Goecks2.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 76 users visited in the last hour