Question: Tophat/Cufflinks for stranded RNA-seq data
0
gravatar for marina.v.yurieva
3.3 years ago by
Farmington, CT
marina.v.yurieva480 wrote:

I have a naive question: what happens if I add "fr-firststrand" option when I run Tophat but don't add it for Cufflinks?

rna-seq • 1.0k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan93k • written 3.3 years ago by marina.v.yurieva480
1
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

If your data is stranded, then you'll get slightly more accurate alignments and novel genes assembled by cufflinks won't have a meaningful strand assigned to them.

ADD COMMENTlink written 3.3 years ago by Devon Ryan93k

Ok, makes sense. Thank you!

ADD REPLYlink written 3.3 years ago by marina.v.yurieva480
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