SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
coveragebed output result problem edge Bioinformatics 2 07-20-2014 11:46 PM
coverageBed giving unordered results at top of list yuchioj Bioinformatics 2 10-24-2012 07:48 AM
coverageBed usagi Bioinformatics 1 01-23-2012 12:13 PM
CIGAR string from BWA-SW output incorrect ? robs Bioinformatics 13 01-13-2012 05:07 AM
MIRA output for Illumina mapping giving 100% coverage! Kasycas Bioinformatics 1 09-10-2010 04:45 AM

Reply
 
Thread Tools
Old 10-29-2012, 11:34 AM   #1
benwittner
Junior Member
 
Location: Boston, MA, USA

Join Date: Jul 2011
Posts: 6
Unhappy coverageBed -split giving incorrect output?

In the command below, coverageBed seems to be ignoring the -split argument.

$ coverageBed -split -a a2.bed -b b2.bed > out.txt

(The inputs and the output for the command above are shown below in addition to being attached.)

Please note that b2.bed defines two blocks, each of width 1960, and that a2.bed defines a single block of length 50 that is between those two blocks and does not intersect them. Yet, in out.txt the 13th field has a 1 in it, indicating that there was an overlap. Also, the 15th field in out.txt is the distance from the beginning of the first block of b2.bed to the end of the last block of b2.bed. I think it should be 1960+1960.

What am I doing wrong? Any help appreciated.
I'm running v2.12.0 of coverageBed.
Thanks. -Ben

$ cat a2.bed
chrX 5561936 5561986 56_1638_1187_F3 50 - 5561936 5561986 255,0,01 50 0

$ cat b2.bed
chrX 4074963 30247441 eg:668963:chrX 0 + 4074963 4076923 0 2 1960,1960, 0,26170518,

$ cat out.txt
chrX 4074963 30247441 eg:668963:chrX 0 + 4074963 4076923 0 2 1960,1960, 0,26170518, 1 50 26172478 0.0000019
Attached Files
File Type: zip coverageBedExample.zip (607 Bytes, 0 views)
benwittner is offline   Reply With Quote
Reply

Tags
coveragebed, split reads

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 10:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO