SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools depth -Q 0 and -Q 1 output discrepancy thedamian Bioinformatics 1 08-03-2016 02:26 PM
Countdata from samtools idxstats dena.dinesh Bioinformatics 6 11-14-2014 05:19 AM
How to use samtools idxstats <bamfile> serhatg Bioinformatics 2 07-02-2014 11:28 PM
samtools idxstats Irina Pulyakhina Bioinformatics 4 10-19-2011 06:05 AM
idxstats option for samtools GenoMax Bioinformatics 0 08-10-2011 07:42 AM

Reply
 
Thread Tools
Old 11-21-2019, 08:09 PM   #1
ndovro
Junior Member
 
Location: Greece

Join Date: Oct 2019
Posts: 1
Question Discrepancy between samtools IDXSTATS and depth

Hi all,
i am baffled from some results and i was wondering if anyone can help.

I am doing RNAseq.

I got my sample, aligned it with STAR on a known reference and used samtools idxstats on the produced sortedbycoord file after indexing.

I get all my contigs/chroms and then run samtools depth for each one of them with -aa.

For some, even though idxstats reports a handful of mapped reads, I get 0 for all the bps with depth.

What am i missing?

Thanks for your time
ndovro is offline   Reply With Quote
Reply

Tags
depth, idxstats, samtools

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 06:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO