I have wig file downloaded from GEO, and since MACS doesn't accept wig file, so I convert it to bed file using wig2bed command. And my bed file looks like this:
chr1 3002399 3002499 id-1 0.110000
chr1 3016999 3017099 id-2 0.110000
chr1 3017099 3017199 id-3 0.110000
chr1 3017199 3017299 id-4 0.110000
chr1 3018699 3018799 id-5 0.110000
chr1 3018799 3018899 id-6 0.110000
chr1 3018899 3018999 id-7 0.110000
chr1 3018999 3019099 id-8 0.110000
chr1 3021699 3021799 id-9 0.110000
chr1 3021799 3021899 id-10 0.110000
But when I run MACS, I get empty output. Is that because the 4th column?
If it is, can someone tell me how to remove it? I tried to use
cut -f 1-3,5 H3K4me1_mef.bed >H3K4me1_mef.bed
and
cat H3K4me1_mef.bed |awk '{print $1 "\t" $2 "\t" $3 "\t" $5}' >H3K4me1_mef.bed
Neither of them works. Is that because they are not separated by tab? But they looks like tab separated.
Thank you for any idea!!!
1 answer
You might save some time by looking at the MACS readme. Seems your BED is missing the required sixth column with strand information. Scroll down to the -f/--format section in the link for more info.
You don't want to remove that fourth column. But just for grins: your command should have worked for a tab-delimited file. It probably won't for a space-delimited file. For a situation where you have multiple separating spaces between columns, I think the easiest course of action is to use:
sed -e 's/[[:blank:]]\+/\t/g' H3K4me1_mef.bed | cut -f 1-3,5 - > H3K4me1_mef_test.bed
This converts all of the interstitial whitespace to a single tab, which cut then handles happily.
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