Question: Strand Specificity
0
Aleks Schein • 60 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
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modified 7.4 years ago
by
Jeremy Goecks • 2.2k
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written
7.4 years ago by
Aleks Schein • 60
