SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
problems visualizing bam files in IGV Line RNA Sequencing 3 04-21-2015 11:33 PM
Problems for cuffdiff output FPKM tracking files Xiaomin Yu Bioinformatics 1 06-13-2012 09:49 PM
Reverse engineering BAM files: BAM -> FASTQ gene coder Bioinformatics 3 01-03-2012 02:42 PM
NEw to Chip-seq and have .bam/.sam/.bam.bai files... then what? NGS newbie Bioinformatics 11 05-25-2011 07:48 AM
the tophat generate the bam file instead of sam files? dingkai0564 Bioinformatics 1 11-10-2010 07:33 PM

Reply
 
Thread Tools
Old 04-11-2012, 12:22 PM   #1
bjchen
Junior Member
 
Location: New York

Join Date: Jan 2012
Posts: 9
Default Problems with Bam files from Tophat

Hi,

I have some troubles with bam files output from tophat and I hope someone here can help me.

1. I have finished running tophat (1.4.1) using UCSC hg19, WITHOUT "--no-sort-bam". But I found the resulting bam files are still sorted as chr1, chr10, chr12...chr2... Did I do anything wrong?

2. So, I can handle the above by using ReorderSam from Picard. But then when I tried to use RNA-SeQC to check the quality, it threw out an exception:

net.sf.picard.PicardException: Found 25613 unpaired mates
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:153)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:169)
at org.broadinstitute.cga.picardbased.CountAligned.getFastQ(CountAligned.java:310)
at org.broadinstitute.cga.picardbased.CountAligned.countBAM(CountAligned.java:115)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.alignAndCountrRNA(ReadCountMetrics.java:209)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:63)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:211)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:162)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:131)


So, I checked the bam file and indeed, I found some reads whose mates are not mapped. My question is, why does tophat output reads whose mates are not mapped? Can I simply remove these "unpaired mapped reads"? How will this affect my downstream analysis?

I will be grateful for any comments or suggestions! Thanks!!
bjchen is offline   Reply With Quote
Reply

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 09:23 PM.


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