macs2 bdgdiff output files

[Chengguo Wei]

Hi Tao,

I used macs2 bdgdiff to call peaks from two different conditions, May I ask what do the columns mean in the output files? I searched a lot but couldn't find the answer.

track type=narrowPeak name="peak" description="peak" nextItemButton=on
chr1	16499	16761	Diff_GFP_WT_encodePeak1	0	.	0	0	0	-1
chr1	17740	18062	Diff_GFP_WT_encodePeak2	0	.	0	0	0	-1
chr1	112608	112840	Diff_GFP_WT_encodePeak3	0	.	0	0	0	-1
chr1	228534	228756	Diff_GFP_WT_encodePeak4	0	.	0	0	0	-1
chr1	325798	326105	Diff_GFP_WT_encodePeak5	0	.	0	0	0	-1
chr1	661373	661581	Diff_GFP_WT_encodePeak6	0	.	0	0	0	-1
chr1	840705	840961	Diff_GFP_WT_encodePeak7	0	.	0	0	0	-1
chr1	853690	853897	Diff_GFP_WT_encodePeak8	0	.	0	0	0	-1

Thanks!

Chengguo

[Alexis Blanchet-Cohen]

I have exactly the same question, which I already posted on this site.

I've copy-pasted the documentation on the mac2 bdgdiff function posted by Tao Liu below.

The problem is that the last column is also always -1 for me also, and not the "the log10 likelihood ratio".

I'd be very grateful if someone could resolve this problem for me.

I've used the latest macs2 bdgdiff from GitHub, and the official release version.

The results are correct, except that there is no means of ranking the peaks outputted by macs2 bdgdiff or distinguishing between them.

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You will get the following three files in working directory:

diff_c1_vs_c2_c3.0_cond1.bed

This file stores regions that are highly enriched in condition 1 comparing to condition 2. The last column in the file represent the log10 likelihood ratio to show how likely the observed signal in condition 1 in this region is from condition 1 comparing to condition 2. Higher the value, bigger the difference.

diff_c1_vs_c2_c3.0_cond2.bed

This file stores regions that are highly enriched in condition 2 comparing to condition 1. The last column in the file represent the log10 likelihood ratio to show how likely the observed signal in condition 2 in this region is from condition 2 comparing to condition 1. Higher the value, bigger the difference.

diff_c1_vs_c2_c3.0_common.bed

This file stores regions that are highly enriched in both condition 1 and condition 2, and the difference between condition 1 and condition 2 is not significant. The last column in the file represent the difference between condition 1 and condition 2 in log10 likelihood ratios.

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[Tao Liu]

Hmm… I believe as for the current 2.0.10.20131216 version ( I just installed it through pip), you got BED file with only five columns, with the format you posted. This is an example:

$head -2 run_bdgdiff_prefix_c3.0_cond1.bed

track name="condition 1 (peaks)" description="unique regions in condition 1" visibility=1

chr1    840081  840332  run_bdgdiff_prefix_cond1_1      7.69809

Do you mind to check the version again?

Best,

Tao Liu

[Alexis Blanchet-Cohen]

Hi Tao, 

Yes, you are absolutely right.

It was entirely my fault.

I wasn't updating the PYTHONPATH environment variable, so I was still using the older 2.0.10.20120913 version, even though I thought I had installed the latest version.

With MACS2 2.0.10.20131216 , I do get just the 5 columns, with the log 10 likelihood ratio in the last column.

Thank you very much for your help.

I'm very happy with the output.

-bash-4.1$ more IP_IC_vs_IP_IC_32_c3.0_cond1.bed

track name="condition 1 (peaks)" description="unique regions in condition 1" visibility=1

gi|555853|gb|U13369.1|HSU13369 98 2298 ../../bdgdiff_humRibosomal/IP_IC_vs_IP_IC_32/IP_IC_vs_IP_IC_32_cond1_1 15.38272

gi|555853|gb|U13369.1|HSU13369 2652 2919 ../../bdgdiff_humRibosomal/IP_IC_vs_IP_IC_32/IP_IC_vs_IP_IC_32_cond1_2 15.81923

Best, 

Alexis