Hi,
I assembled transcripts using TopHat/Cufflinks pipeline using Illumina paired-end RNA-Seq reads. I am working with human transcriptome data. When I compared Cufflinks assembled transcripts with the RefSeq transcripts, I found that some of the assembled transcripts have alternative 3'ends. My plan is to validate these alternative 3'ends by aligning the original RNA-Seq reads to the assembled transcripts using BowTie or BWA and look for homopolymer(A or T) stretches.
My confusion is about the read orientation. Should I look for poly T heads or polyA tails (or both poly T and poly A tails) in order to validate alternative 3' ends in assembled transcripts?
Any thoughts?
I assembled transcripts using TopHat/Cufflinks pipeline using Illumina paired-end RNA-Seq reads. I am working with human transcriptome data. When I compared Cufflinks assembled transcripts with the RefSeq transcripts, I found that some of the assembled transcripts have alternative 3'ends. My plan is to validate these alternative 3'ends by aligning the original RNA-Seq reads to the assembled transcripts using BowTie or BWA and look for homopolymer(A or T) stretches.
My confusion is about the read orientation. Should I look for poly T heads or polyA tails (or both poly T and poly A tails) in order to validate alternative 3' ends in assembled transcripts?
Any thoughts?