Question: Will pseudoaligners detect rearrangements based on known transcripts?
0
gravatar for b10hazard
22 months ago by
b10hazard30
United States
b10hazard30 wrote:

I have a question about pseudo aligners. I’m using Kallisto and I was wondering if it would count novel rearrangements of known transcripts. For example, suppose I have the following gene consisting of three exons.

EXON1----EXON2-------------------EXON3

If I include this in the kallisto transcriptome and index it I understand that Kallisto will detect and count the intended transcript such as this…

EXON1-EXON2-EXON3

My question is.... What if there were a transcript like this in which the second exon was missing….

EXON1-EXON3

Would Kallisto detect and include this in the gene counts?

What about if exon 2 and 3 were swapped, like this…

EXON1-EXON3-EXON2

ADD COMMENTlink written 22 months ago by b10hazard30
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: 1173 users visited in the last hour