SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
fastest solution to get bam2fastq done memento Bioinformatics 34 05-31-2014 03:51 AM
Tophat reads kept/discarded during initial conversion kreitinger Bioinformatics 8 10-05-2013 12:27 AM
Bam2FastQ help Zapages Bioinformatics 4 10-30-2012 03:18 AM
duplicate reads in Illumina short, single end reads of RNAseq data inbarpl Bioinformatics 4 05-22-2012 08:36 AM
bam2fastq wangli RNA Sequencing 0 04-19-2012 08:20 AM

Reply
 
Thread Tools
Old 01-14-2013, 03:31 AM   #1
Derek-C
Junior Member
 
Location: U.S.A.

Join Date: Nov 2012
Posts: 7
Default bam2fastq discarded reads

Hi all,

I've been using bam2fastq on my tophat output and it's been great, runs really quickly, except for the number of reads being discarded. For example this was for one of my output files from tophat

This looks like paired data from lane 239.
Output will be in x_1.fastq and x_2.fastq
60465861 sequences in the BAM file
60465861 sequences exported
WARNING: 6585459 reads could not be matched to a mate and were not exported

That's 10% of the reads being discarded, and in other files it's even more (I ran it on another file just now and 17% of the reads were discarded). What I don't understand is that the PE files which were put into tophat were quality filtered with software to directly handle PEs and so both files have the same number of reads and all the reads have mates and both PE files are the same order (tophat freaks out otherwise) so why is bam2fastq discarding these reads? If any reads didn't have a mate then tophat would have returned an error.

Last edited by Derek-C; 01-14-2013 at 03:47 AM.
Derek-C is offline   Reply With Quote
Old 01-14-2013, 03:50 AM   #2
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

I remember Bam2fastq only export read pair. So, all singleton mapped will be discarded. In your case, it may be better to write a small script to parse the singleton out
__________________
Marco
marcowanger is offline   Reply With Quote
Old 01-14-2013, 06:01 AM   #3
Derek-C
Junior Member
 
Location: U.S.A.

Join Date: Nov 2012
Posts: 7
Default

Quote:
Originally Posted by marcowanger View Post
I remember Bam2fastq only export read pair. So, all singleton mapped will be discarded. In your case, it may be better to write a small script to parse the singleton out
Are you certain about the singletons thing? It would make sense, butl I just did some checking there with samtools flagstat and according to the numbers I'm looking at for this one accepted_hits.bam file from tophat there were more singleton reads then there were reads discarded by bam2fastq (~3 million more). So if bam2fastq doesn't export singletons, what happened to those 3 million reads.

Actually there are options in tophat for setting it so that there should be no singletons, hopefully that'll fix this.

Last edited by Derek-C; 01-14-2013 at 06:29 AM.
Derek-C is offline   Reply With Quote
Reply

Tags
bam2fastq, tophat

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 06:44 PM.


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