merge BED files from two lanes?

[alittleboy]

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:

junctionBedFilesControl=c(
"/path/to/junctionsBed_sample_1.bed",
"/path/to/junctionsBed_sample_2.bed",
"/path/to/junctionsBed_sample_3.bed")
junctionBedFilesCancer=c(
"/path/to/junctionsBed_sample_4.bed",
"/path/to/junctionsBed_sample_5.bed",
"/path/to/junctionsBed_sample_6.bed")

expInf=setJunctionBedFiles(expInf,c(junctionBedFilesControl,junctionBedFilesCancer))

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!

[pengchy]

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.