Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to merge two vcf files. cardillox Bioinformatics 3 11-27-2019 09:25 PM
merge gbk files krispy Bioinformatics 14 08-29-2016 02:48 AM
Splitting a bed file in multiple bed files by track albireo Bioinformatics 3 12-18-2014 11:58 AM
RG tags in merged BAM files, muliple lanes one sample cow_girl Bioinformatics 17 08-27-2013 11:28 PM
Merge Fasq Files yagoubali Illumina/Solexa 0 12-13-2012 05:45 PM

Thread Tools
Old 06-27-2013, 09:37 AM   #1
Location: USA

Join Date: Apr 2011
Posts: 60
Default merge BED files from two lanes?

Hi, I am using SplicingCompass for testing differential exon usage, and one step involved is to use BED files for each of the biological samples, as shown in the manual:



My question is, since for each sample, I sequenced for two lanes in TopHat, so that I have two junctions.bed file for each biological samples. Should I merge these two BED files from 2 lanes into one? If so, what tools should I consider? Bedtools? I saw some people suggested:

cat junctions1.bed junctions2.bed | mergeBed -i stdin

Also, I notice there a related post here: in the last thread, the author suggested using

cat junctions_file1.bed junction_file_2.bed junction_file_3.bed | tbed2juncs | combineJuncs > combined.juncs

from the tools downloaded here. "combine.juncs will be a BED file and contains all of the junctions from the junction files with the score the sum of the junction scores." -- just curious if this .juncs file can be used the same as the .bed file from TopHat output?

Thanks so much!

Last edited by alittleboy; 06-30-2013 at 01:37 PM.
alittleboy is offline   Reply With Quote
Old 08-19-2013, 12:25 AM   #2
Senior Member
Location: China

Join Date: Feb 2009
Posts: 116

The .juncs file is not the same as the .bed file from TopHat output in the following:
1. they are in different format.
2. .juncs files only contain the coordination and score, the block length has been filtered.

However, if you don't care the block length, you can make a junctions.bed file yourself with the output file of combineJuncs.

Last edited by pengchy; 08-19-2013 at 12:30 AM.
pengchy is offline   Reply With Quote

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 06:57 PM.

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