Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
converting between genome and transcripts coordinates leshkowitz Bioinformatics 3 04-02-2018 05:55 PM
Quantifying whole genome PCR-free libs without qPCR EGraf Sample Prep / Library Generation 3 10-05-2015 03:53 PM
Viral genome vs transcripts vijesh Bioinformatics 5 06-14-2013 12:20 AM
fill gaps in genome by transcripts neurospora Bioinformatics 2 08-28-2012 12:47 AM

Thread Tools
Old 08-21-2018, 09:34 PM   #1
Junior Member
Location: canada

Join Date: Oct 2009
Posts: 4
Default quantifying transcripts in a redundant genome


I am trying to quantify the number of reads mapping to genes in a highly redundant bacterial genome (i.e., often several exact gene copies in the genome).

I've mapped reads to genes with bbmap, and quantified using featurecounts. My problem is that reads are only counted for one of the copies of redundant genes, and not all of them.

I just want to count the number of expressed genes (I want to count all of the copies since I can't distinguish them). I've tried playing around with multi-mapping parameters in featurecounts, but nothing has changed.

Does anyone here know how to do this?

garlic is offline   Reply With Quote
Old 08-31-2018, 06:50 AM   #2
Junior Member
Location: Ann Arbor

Join Date: Aug 2018
Posts: 2

You would have to play with your aligner (bbmap). I've never used that one before, but other aligners like bowtie2 and BWA have an option to search for multiple alignments and report all. However, if you do this, you will be overestimating expression of your redundant genes.
ASintsova is offline   Reply With Quote

bacteria genome, bbmap, featurecounts, read mapping, transcriptome

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:13 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO