How to derive sequence of novel transcript identified by Cufflinks
I am new to transcript level analysis using RNA-Seq. The goal is to retrieve sequence of newly identified transcript from RNA-Seq data. We just finished runing Cufflinks and seems like that a number of putative novel transcripts were generated. What do I have to do to further retrieve the sequence of novel transcript? Or at least recognize the exons included in novel transcripts? Thanks
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How do you find novel transcripts using GFFcompare?
written by c_u
-
gffcompare class code 'j'
written by waqaskhokhar999
-
Using Cufflinks for Novel Transcripts
written by Ron
-
Understanding the gffcompare output for my dataset
written by amy16 •
-
how to find novel genes and transcripts in gffcompare?
written by naveenkumarv40 •
-
How to get an XS field in SAM with unstranded data ?
written by corend
-
Cuffmerge potential error
written by moustafa_abohawya •
-
recognize known isoform from transcript mapping
written by ghbore •
-
Discovery of novel transcripts
written by hana
-
Manual Transcriptome Reconstruction Using Rna-Seq Reads (Hg19)
written by biorepine
do you have a reference transcriptome/genome at your disposal?
Yes, it is reference guided.
in that case you can align your reads to the reference and then subtract all the ones that align to known genes and the leftover are the novel ones.
or is this not what you're asking for?