Question: Studying variances in assembled transcripts
0
gravatar for rmihael
4.3 years ago by
rmihael0
rmihael0 wrote:

Hi all. This is my first steps in bioinfomatics, so please forgive me for potentially trivia questions.

I'm trying to study variations in transcripts of a same gene on different developmental stages of dmel flies. In particular I want to verify the hypothesis that 3' UTRs are shortened at latest developmental stages. Obvious intermediate step of this study is obtaining transcript from assembled RNA-Seq data. This is where I have my problems.

After mapping with Tophat and assembling with Cufflinks my final result is transcripts.gtf file. I can use gffread as

gffread -g dmel.bowtie.index.fa -w transcripts.fa cufflinks_out/transcripts.gtf

to get aligned transcripts, but these transcripts will be from reference genome, so stripped of any potential variations.

So, the question is, how can I get these "raw" transcripts that were aligned by cufflinks from sequencing data? It sounds like a de novo alignment problem, but there IS reference genome and annotation available, so may be it's possible to take advantage of it?

rna-seq • 1.5k views
ADD COMMENTlink written 4.3 years ago by rmihael0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 884 users visited in the last hour