Question: Tophat/Cufflinks for stranded RNA-seq data
0
gravatar for marina.v.yurieva
4.1 years ago by
Farmington, CT
marina.v.yurieva520 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 • 1.1k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan96k • written 4.1 years ago by marina.v.yurieva520
1
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k 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 4.1 years ago by Devon Ryan96k

Ok, makes sense. Thank you!

ADD REPLYlink written 4.1 years ago by marina.v.yurieva520
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