SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat paired end read alignment idyll_ty Bioinformatics 0 02-18-2012 09:58 PM
Tophat paired end alignment. adeslat SOLiD 5 08-07-2011 03:05 AM
how paired end alignment works? totalnew Bioinformatics 8 04-27-2009 12:46 PM
why is paired-end alignment support so important found Bioinformatics 1 03-03-2009 07:05 AM

Reply
 
Thread Tools
Old 03-01-2018, 05:45 PM   #1
Mark
Member
 
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 48
Default BBMAP paired-end alignment problem

Hi All

I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.

Execution of

Code:
bbmap.sh overwrite=t ref=Z.fasta in=R1_001_val_1.100.fq in2=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam  outu=unaligned_reads.fa maxindel=100000
yields out.sam which contains only alignments of read1 even though the log info seems to suggest read2 reads were also aligned

Code:
Pairing data:           pct reads       num reads       pct bases          num bases

mated pairs:            100.0000%             100       107.4763%              59558
bad pairs:                0.0000%               0         0.0000%                  0
insert size avg:          412.82


Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                 100.0000%             100       100.0000%              29779
unambiguous:            100.0000%             100       100.0000%              29779
ambiguous:                0.0000%               0         0.0000%                  0
low-Q discards:           0.0000%               0         0.0000%                  0

perfect best site:        0.0000%               0         0.0000%                  0
semiperfect site:        35.0000%              35        35.1758%              10475
rescued:                  0.0000%               0

Match Rate:                   NA               NA        88.8176%              26449
Error Rate:              65.0000%              65         4.4763%               1333
Sub Rate:                65.0000%              65         0.3627%                108
Del Rate:                 0.0000%               0         0.0000%                  0
Ins Rate:                49.0000%              49         4.1136%               1225
N Rate:                 100.0000%             100         6.7061%               1997


Read 2 data:            pct reads       num reads       pct bases          num bases

mapped:                 100.0000%             100       100.0000%              25636
unambiguous:            100.0000%             100       100.0000%              25636
ambiguous:                0.0000%               0         0.0000%                  0
low-Q discards:           0.0000%               0         0.0000%                  0

perfect best site:        0.0000%               0         0.0000%                  0
semiperfect site:        26.0000%              26        25.3745%               6505
rescued:                  2.0000%               2

Match Rate:                   NA               NA        86.8232%              22258
Error Rate:              74.0000%              74         4.9852%               1278
Sub Rate:                74.0000%              74         0.8894%                228
Del Rate:                 0.0000%               0         0.0000%                  0
Ins Rate:                42.0000%              42         4.0958%               1050
N Rate:                 100.0000%             100         8.1916%               2100
As a test I then tried

Code:
bbmap.sh overwrite=t ref=Z.fasta in=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam  outu=unaligned_reads.fa maxindel=100000
Here read2 reads were aligned.

Any ideas what is wrong with the first command line for the paired-end reads?

Thanks

Mark
Mark is offline   Reply With Quote
Old 03-02-2018, 08:30 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,794
Default

Cross-posted and answered on Biostars:https://www.biostars.org/p/301541/
GenoMax is online now   Reply With Quote
Reply

Tags
align, bbmap, paired-end

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 09:02 AM.


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