coupling Cufflinks results with RSEM
Hello!
I am opening this post to ask if I can use the transcript-level assembly obtained with Cufflinks (using a reference genome) to independently quantify the abundance levels of these sequences with RSEM (transcript-level quantification), specifically designed to quantify isoforms. Subsequently, I would perform differential expression (DE) analysis with DeSeq2.
Is this correct? Or should I use the quantifications obtained with Cufflinks for the DE analysis?
Thanks in advance
• 737 views
•
link
written
by
sofiablancoglez •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Low mapping after Cufflinks assembly
written by sofiablancoglez •
-
Summarizing transcript level annotation from Trinity de novo assembly to gene level annotation
written by MB •
-
RSEM isoform.results outputs for edgeR
written by weichengz •
-
How to select the best isoform for a differential expressed gene in Trinity?
written by upendrakumar.devisetty
-
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
written by tianshenbio
-
Is Stringtie a suitable tool for both gene and transcript quantification?
written by tianshenbio
-
How is the bootstrapping information from kallisto treated in DeSeq2 when imported using tximport?
written by divya.nandakumar •
-
Performing differential expression study on isoforms
written by glady
-
Calculating isoforms abundance using RNAseq data
written by iditk •
-
Cuffdiff2 Gene Level Quantification
written by narges •
