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.
1 answer
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
Log in to answer this question.
-
ChIPseeker annotation
written by sk_24 •
-
Chipseq peak calling and peak frequency region
written by mavy •
-
Question about ChIPseeker parameters
written by Jen •
-
ChIP-seq; investigate binding within region of tRNA genes
written by 2138493o •
-
How to compare the peaks called by MACS2 with the peaks called by ChIPOTLe?
written by s.singh •
-
Sorting .bed file by genes size
written by Marco Pannone •
-
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
written by mrj •
-
Chip-Seq peaks annotation
written by tarek.mohamed
-
Chipseq peak analysis using ChIPseeker
written by Mike
-
ChIP peak data set comparison
written by s.singh •
Please show an example of that file you have. BED is in fact a tabular format.
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....