I'm hoping that someone can help me, as I couldn't work out how to do
this from the manual. Would someone be able to give me the steps in a
differential expression analysis?
I have run tophat with the following command for each of my two solexa
sequence.txt RNA-seq files seperately:
tophat -solexa1.3-quals -p 2 -o 101/100315/tophat/
101/100315/s_2_sequence.txt &> 101/100315/tophat/tophat.out &
I would like to get the expression levels for all Ensembl transcripts.
I have downloaded this gtf file from Ensembl,
However when I run
&> cuffdiff.out &
cufflinks -G ~/data/gtf/Mus_musculus.NCBIM37.57.gtf 101/100315/tophat/accepted_hits.sam &>
I get the following error
Error: duplicate GFF ID 'ENSMUST00000127664' (or exons too far apart)!
I'm pretty sure I've misunderstood the workflow, if someone could give me
an overview of the steps and what gtf file I should be using that would
(Cross posted to SeqAnswers)
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