Viewing PET data in IGV

dphansti · 03-07-2012, 06:32 PM

I have a bed file from PET data in this format

chr17 58754953 58754971 pair1 23 -
chr17 58755650 58755672 pair1 25 +
chr13 93209287 93209313 pair2 37 +
chr13 93209438 93209457 pair2 20 -

etc.

I want to plot it in IGV so each pair is represented as it is in the attached figure where each read is represented as a box with a line connecting the two members of each pair. What format do I need to convert my data into? Or how can I view it this way.

dphansti · 03-07-2012, 06:41 PM

Nevermind. I figured it out. I made a .gff file and treated each pair like an exon from a gene.

Jim Robinson · 03-13-2012, 03:13 AM

Hi,

That will work, you can also use bed format but you have to use the extended form. See the UCSC site for details. BED files have the advantage of being much smaller, in general, and can also be indexed or converted to "bigBed".

Jim

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Viewing Tophat results in IGV	SEQquestions	Bioinformatics	19	10-17-2014 12:12 PM
Dindel SAM/BAM format - viewing with IGV	EHC	General	0	10-06-2011 11:27 AM
problem of viewing assembly data in Tablet	percy	Bioinformatics	4	09-15-2010 07:42 AM
Viewing GFF2/GFF3 files on IGV	pratibhamani	SOLiD	1	02-04-2010 08:54 AM
ChIP - PET data analysis	bogdan	Bioinformatics	0	05-18-2009 05:42 PM

03-07-2012, 06:41 PM	#2
dphansti Member Location: Bay Area Join Date: May 2011 Posts: 28	Nevermind. I figured it out. I made a .gff file and treated each pair like an exon from a gene. __________________ Doug www.sharedproteomics.com

03-13-2012, 03:13 AM	#3
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi, That will work, you can also use bed format but you have to use the extended form. See the UCSC site for details. BED files have the advantage of being much smaller, in general, and can also be indexed or converted to "bigBed". Jim