SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Counting reads (not coverage...) smol Bioinformatics 4 08-24-2016 05:11 AM
counting junction reads in TopHat schaffer Bioinformatics 3 10-21-2011 01:05 AM
Counting Reads in SAM Format foolishbrat General 2 06-08-2011 12:38 PM
Counting reads that jump over a position DerSeb Bioinformatics 0 01-17-2011 06:05 AM
Question on counting number of reads per gene gen2prot Bioinformatics 3 06-25-2010 10:45 AM

Reply
 
Thread Tools
Old 02-10-2012, 11:09 AM   #1
muzz56
Member
 
Location: Boston

Join Date: Sep 2010
Posts: 14
Default counting junction reads

I bet someone has asked this question before, but I'll ask it anyway. I have run Tophat and have the accepted hits bam file and the juntions.bed file. I'd like to know the number of reads in the bam file aligning to each junction coordinate in the bed file. I have tried to use bedtools with no success. Does anyone have any idea how to achieve this?. Essentially I'd like to know only the number of reads aligning to junctions.
Regards.
muzz56 is offline   Reply With Quote
Old 02-10-2012, 07:40 PM   #2
malcook
Member
 
Location: 66206

Join Date: Sep 2009
Posts: 23
Default

http://malcook-gedanken.blogspot.com...-reads_09.html
malcook is offline   Reply With Quote
Old 02-12-2012, 05:36 AM   #3
muzz56
Member
 
Location: Boston

Join Date: Sep 2010
Posts: 14
Default

Thanks for the reply. I am just wondering what the input files to this script will be?. Since I'll source the script, I'd like to include the paths to the input files in the script but don't know which inputs are required. R is not my cup of tea so forgive me if this is clear from the script.
muzz56 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 05:21 PM.


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