SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA properly paired reads are not really properly paired? metheuse Bioinformatics 0 06-19-2015 11:29 AM
High Percentage of Soft Clipping, BWA-MEM, MiSeq logicthief Bioinformatics 9 09-11-2014 06:19 PM
BWA: paired end reads, wrong orientation but listed as properly paired rdeborja Bioinformatics 3 06-11-2014 04:39 AM
why the properly paired results from bwa mem is an odd number Pengfei Liu Bioinformatics 2 08-24-2013 07:26 PM
Lower percentage of properly paired sequence sunnyvu Bioinformatics 3 05-12-2010 09:58 AM

Reply
 
Thread Tools
Old 09-28-2020, 04:45 PM   #1
mglasenapp
Junior Member
 
Location: Santa Cruz, California

Join Date: Sep 2020
Posts: 1
Default bwa mem - low properly paired percentage

After aligning paired-end 100bp reads to a reference genome, I am getting very low properly paired percentage:

369208441 0 total (QC-passed reads + QC-failed reads)
8985531 0 secondary
289733341 0 mapped
78.47% N/A mapped %
360222910 0 paired in sequencing
180111455 0 read1
180111455 0 read2
1393338 0 properly paired
0.39% N/A properly paired %
280747810 0 with itself and mate mapped
0 0 singletons
0.00% N/A singletons %
39590468 0 with mate mapped to a different chr
0 0 with mate mapped to a different chr (mapQ>=5)

I followed GATK best practices to align paired-end short-read data to a reference genome. I downloaded the short-read data from NCBI SRA into fastq files using SRA toolkit's fastq-dump, converted the fastq files into unmapped bam using Picard FastqToSam, and marked adapters using Picard MarkIlluminaAdapters. I then piped Picard SamToFastq, bwa mem, and Picard MergeBamAlignment. To get stats on the alignment, I used samtools flagstat. For several of my samples, the alignment went great (90% mapped, 80% properly paired). However, for a couple of my samples, the properly paired percentage was well below 1%. I'm wondering how I could have a normal amount of reads mapping (~78%) but have only .39% of those reads properly paired.

I have double-checked that my fastq files from fastq-dump have identical read counts, and that they are properly interleaved after Picard FastqToSam.
mglasenapp is offline   Reply With Quote
Old 09-29-2020, 03:30 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

Cross-posted at biostars: https://www.biostars.org/p/464101/
GenoMax is offline   Reply With Quote
Old 10-11-2020, 05:54 AM   #3
elmtnakl
Junior Member
 
Location: المدينة

Join Date: Oct 2020
Posts: 1
Default

https://www.elmtnakl.com/H1/moving-furniture-in-madinah
https://www.elmtnakl.com/H1/transfer-furniture-jazan
https://www.elmtnakl.com/H1/transfer-furniture-ahsa
https://www.elmtnakl.com/H1/transfer-furniture-mecca
https://www.elmtnakl.com/H1/moving-furniture-sharorh
https://www.elmtnakl.com/H1/transfer...khamis-mushait
https://www.elmtnakl.com/H1/transfer-furniture-yanbu
https://www.elmtnakl.com/H1/transfer-furniture-alkharj
https://www.elmtnakl.com/H1/transfer-furniture-abha
https://www.elmtnakl.com/H1/transfer-furniture-buraydah
https://www.elmtnakl.com/H1/Moving-furniture-in-Dammam
https://www.elmtnakl.com/H1/transfer...ture-in-najran
https://www.elmtnakl.com/H1/Moving-furniture-in-Riyadh
https://www.elmtnakl.com/H1/transfer-furniture-tabuk
https://www.elmtnakl.com/H1/moving-furniture-in-jeddah
https://www.elmtnakl.com/H1/transfer-furniture-hail
https://www.elmtnakl.com/H1/transfer-furniture-qatif
https://www.elmtnakl.com/H1/transfer-furniture-bahah
https://www.elmtnakl.com/H1/transfer-furniture-in-arar
https://www.elmtnakl.com/H1/transfer...-hafr-al-batin
https://www.elmtnakl.com/H1/transfer...re-mahail-asir
https://www.elmtnakl.com/H1/transfer-furniture-qassim
https://www.elmtnakl.com/H1/moving-furniture-in-unayzah
https://www.elmtnakl.com/H1/transfer-furniture-taif
https://www.elmtnakl.com/H1/moving-furniture-in-khobar
https://www.elmtnakl.com/H1/furniture-transfer-gebeel
https://www.elmtnakl.com
https://www.elmtnakl.com/H1
https://www.elmtnakl.com/H2
https://www.elmtnakl.com/H3
https://www.elmtnakl.com/H4
https://www.elmtnakl.com/H5
https://www.elmtnakl.com/H6
elmtnakl is offline   Reply With Quote
Reply

Tags
bwa alignment, gatk alignment pipeline, samtools flagstat

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 07:43 AM.


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