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!
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!

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