SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
fastq.gz stats READ-COUNT BASE-COUNT jgibbons1 Bioinformatics 9 10-30-2013 05:24 AM
Changing read names stepa_t Bioinformatics 4 03-04-2013 02:59 AM
Plotting ChIP-seq read profiles relative to genomic features Gilman85 Bioinformatics 7 12-07-2012 09:45 AM
SAM/BAM sort by read names produces truncated read names allenyu Bioinformatics 7 09-24-2012 10:46 PM
SFF Read names johan 454 Pyrosequencing 8 04-19-2012 07:54 AM

Reply
 
Thread Tools
Old 02-04-2014, 10:37 PM   #1
foolishbrat
Member
 
Location: South East Asia

Join Date: Nov 2008
Posts: 44
Default Tools that report read count AND read names that map to genomic features.

htseq-count and coverageBed are excellent tools for reporting just how many reads map to each genomic features.

How ever to my knowledge the could not report the read names that correspond to the count. Is there any tools that does that?
foolishbrat is offline   Reply With Quote
Old 02-05-2014, 12:21 AM   #2
BenB
Junior Member
 
Location: Cologne, Germany

Join Date: Feb 2014
Posts: 1
Default

Hi,
if you use the "-o" option of htseq-count you generate a sam file that contains an extra column "XF" that contains the feature for each read alignment. Maybe that is what you are looking for?

You can simply create a tab delimited file using "cut -f1,15 <SAM>" from this file telling you which read corresponds to which feature.

Ben
BenB is offline   Reply With Quote
Reply

Tags
alignment, bam, genomic features, read count, sam

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 08:45 AM.


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