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Intersectbed of Homer and MAcs2 peak caller results

Hello, I am trying to compare a Homer .txt file and Macs2 .bed file using intersectbed. I have tried to convert .txt file to a .bed file so that it works, but was unable to find a way to do it. When I try to perform the intersectbed of the two files it gives me an illegal binCall error. Moreover, I have modified the .txt file to remove the extra info and certain columns but to no avail.

Is there anything I could do to resolve this issue?

software error chip-seq alignment
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written by bulkybogany • bulkybogany

illegal binCall error. means the file is not properly tab-delimited. Please show representative input and how you modified the files.

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written by ATpoint ATpoint

Code for Homer file (dir and base being my directory and file to be processed respectively): findPeaks ${dir}/${base} -style factor -gsize 2700000000

Code for Macs2 file (dir and base are different than ones used for the previous script): macs2 callpeak -t ${dir}/${base}_sorted.bam -f BAMPE -g 2.7e9 -n $base --outdir $dir2 --bdg

Code for intersectbed and formatting (same thing with dir and base): sed -e '1,/#PeakID/d' ${dir2}/${base2}.txt > ${dir2}/${base2}.convert head -n -2 ${dir2}/${base2}.convert > ${dir2}/${base2}.convert1 awk '{$1=$5=$6=$6=$7=$8=$10=$11=""; print $0}' ${dir2}/${base2}.convert1 > ${dir2}/${base2}.done bedtools intersect -a ${dir}/${base}_summits.bed \ -b ${dir2}/${base2}.done

.txt is the Homer file, _summits.bed file is the Macs2 file, .done is the modified Homer file where I removed a couple of lines that were deemed unnecessary, as well as the columns that were absent in the Macs2 file.

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written by bulkybogany • bulkybogany

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