Question: How can I know if a new transcript was assembled in a specific or both conditions in merge GTF file?
gravatar for tawares07
2.2 years ago by
tawares070 wrote:

Hi guys!

I have a question in how to interpret StringTie results using the protocol published in Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown:

O followed the protocol assembling transcripts (step 3), merging all results (step 4) and restimating transcript abundances (step 6). After this last step, I wanted to know if an assembled transcript was present in normal and/or tumoral conditions.

So, I looked in the merge file and I identified annotated transcripts and potential new assemblies . For annotated transcripts I could identify where they were assembled (normal and/or tumoral condition) searching the ENSEMBL ID in the GTF file of each sample created in step6. However, I could not do the same thing for the new assemblies.

My question is: how can I know if a new transcript was assembled in a specific or both conditions?

ADD COMMENTlink written 2.2 years ago by tawares070
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1109 users visited in the last hour