SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
one gene one RPKM cufflinks or DEseq frankyue50 Bioinformatics 5 10-30-2014 12:37 AM
Tophat -> Cufflinks: BAM header too large peromhc Bioinformatics 9 08-06-2013 01:29 PM
RPKM and multiple reads, tophat and cufflinks mgogol Bioinformatics 6 09-03-2012 02:46 PM
some gene no RPKM in every library by Cufflinks stunlay RNA Sequencing 0 08-19-2011 09:06 AM
Cufflinks crashes on BAM output from TopHat Sherry Bioinformatics 0 02-07-2011 07:04 AM

Reply
 
Thread Tools
Old 04-26-2010, 07:59 AM   #1
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default tophat/cufflinks bam vs. RPKM

Is there any legitimate reason a tophat bam file would have reads for a gene whose RPKM was not reported in the output from tophat or cufflinks?
mgogol is offline   Reply With Quote
Old 04-26-2010, 09:08 AM   #2
thinkRNA
Member
 
Location: Carlsbad,CA

Join Date: Jan 2010
Posts: 94
Default

Quote:
Originally Posted by mgogol View Post
Is there any legitimate reason a tophat bam file would have reads for a gene whose RPKM was not reported in the output from tophat or cufflinks?
You are finding reads in tophat bam file that are not reported in output from tophat (which is .bam format)? I don't really understand your question-can you give an example.
I thought tophat uses FPKM units and not RKPM.
thinkRNA is offline   Reply With Quote
Old 04-26-2010, 09:16 AM   #3
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

If I look at the list of genes whose FPKMs are reported by cufflinks, a certain group of genes is not found in that list at all.

If I load a bam file generated from the tophat sam file into IGV, and browse around looking at those genes, they have reads. So they have reads, but FPKMs are not reported.

I'm just wondering if this an error or if there is some legitimate explanation?
mgogol is offline   Reply With Quote
Old 04-26-2010, 09:29 AM   #4
thinkRNA
Member
 
Location: Carlsbad,CA

Join Date: Jan 2010
Posts: 94
Default

if the reads are too few, they may be filtered by the F/--min-isoform-fraction parameter where TopHat filters out junctions supported by too few alignments.
May be you can set it to 0.

Also, I don't intuitively understand -a/--min-anchor-length <int> parameter, but it may also be limiting your reads that are counted for the FPKM.
thinkRNA is offline   Reply With Quote
Old 04-26-2010, 09:52 AM   #5
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

Thanks for the ideas.
mgogol is offline   Reply With Quote
Old 04-26-2010, 09:58 AM   #6
thinkRNA
Member
 
Location: Carlsbad,CA

Join Date: Jan 2010
Posts: 94
Default

sure, if you find out whats going on, let us know. If the reads you saw on IGV don't span junctions, then its probably a parameter in bowtie that is throwing it- off-low quality or reads mapping to multiple places in the genome or something else. Its a good thing you caught it though
thinkRNA 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 04:32 PM.


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