SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Illumina pair end read extraction. JDinis Bioinformatics 3 06-06-2012 08:00 PM
What is the longest fragment for Illumina Mate pair end seq library? ychang Sample Prep / Library Generation 4 03-08-2012 12:11 AM
Using MAQ to simulate illumina pair-end reads yjx1217 Bioinformatics 0 10-27-2011 08:38 AM
Illumina Pair end primers and adaptors for multiplexing mimi_lupton Sample Prep / Library Generation 1 05-25-2011 07:57 AM
Illumina Pair end library protocol Berkeley2010 Illumina/Solexa 16 11-18-2010 06:53 AM

Reply
 
Thread Tools
Old 11-30-2015, 10:59 AM   #1
c_ro87
Member
 
Location: Buenos Aires

Join Date: Feb 2012
Posts: 12
Default Illumina Truseq Pair end

Hello, I have data from a custom truseq design.

The reads alignment was done using BWA, and variant calling using GATK following the best practices.

From the image, the bottom panel shows the alignment for the data after realignment around indels and score recalibration, you can see a peak in the midlle where coverage is the double than in both sides. This is the portion where the pairs overlapp, my first question is, if this is a normal behaviour, or maybe i'm too restrict when do my adapters removal?
This is the command line i use:
../../../../bin/fastq-mcf -o SAR093-2015/SAR093-2015-01-00001_S2_L001_R1_001_adap.fastq -o SAR093-2015/SAR093-2015-01-00001_S2_L001_R2_001_adap.fastq -l 50 -q 20 -x 10 -u -P 33 ../../../../data/adaptadores_truseq/adaptadores.txt SAR093-2015/SAR093-2015-01-00001_S2_L001_R1_001.fastq SAR093-2015/SAR093-2015-01-00001_S2_L001_R2_001.fastq &>r.log

The upper panel is the bamout generated after the GATK variant calling, and this show that the left part of the reads now is missing, any comments on this?

c_ro87 is offline   Reply With Quote
Reply

Tags
gatk, haplotype, variant calling

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 09:09 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO