How to annotate a MACS2 peak output file that is in tabular format?

Question

[Jen]

I am fairly new to ChIP-seq analysis. I am using data from someone else and they only have the MACS2 peak file in tabular format. I have annotated peaks previously using MACS2 .bed files using ChIPseeker, but am unsure of how to go about annotating the tabular peak file. Can I convert this into bed somehow? Is there another way I should go about this? The tabular file has the genomic locations, so I'm assuming there is an easy way to go about doing this. Thanks in advance.

[ATpoint]

Please show an example of that file you have. BED is in fact a tabular format.

[Jen]

[Jen]

I'm just confused because the person provided both .bed and this tabular file for MACS2 for their other samples. Sorry if there is an obvious solution here....

Answer 1

[jv]

BED files are tab-delimited so that's not the real issue here.

You already have all the info you need to convert this to a BED file, but you need to keep in mind that BED files (and bedgraphs too) use a 0-based coordinate system and the stop coordinate is exclusive.

Ultimately the only change you need to make is to subtract 1 from the start position and leave the stop position as is. For example, the first peak in your example here would look like the following in bed format:

chr1 44270098 4427779

For more details on BED file format see https://genome.ucsc.edu/FAQ/FAQformat.html#format1

[Jen]

Got it. Thanks!