SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Counting Reads in BAM file per genomic position C9r1y Bioinformatics 4 11-24-2015 03:11 PM
Counting Reads in BAM file by Region CodeHippo Bioinformatics 4 03-24-2014 01:03 PM
tool for counting A T G C in a bam sirmark Bioinformatics 2 04-15-2013 05:29 AM
counting tags in bam file james4545 Bioinformatics 2 01-10-2013 09:03 AM
Counting mapped nucleotides in a bam file moriah Bioinformatics 7 08-22-2011 02:30 AM

Reply
 
Thread Tools
Old 07-11-2017, 08:36 AM   #1
NDUFB11
Junior Member
 
Location: Italy

Join Date: Jul 2017
Posts: 7
Default BAM alignment and counting

Hello everyone,
Can you tell me which is the most common way to quantify the reads from an RNAseq bam file?
Other that futureCounts, is there anything else well know and reliable?

Thanks
NDUFB11 is offline   Reply With Quote
Old 07-12-2017, 12:14 AM   #2
wdecoster
Member
 
Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 95
Default

featureCounts and htseq-count are the most commonly used tools, but you could also use Salmon (with or without alignment) or kallisto (without alignment).
wdecoster is offline   Reply With Quote
Reply

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 07:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO