what does the bed file in bedtools multicov command refer to ?

Question

[rania.hamdy1]

Dear bedtools users,

Hope everything is well with you

I want to use multicov mode to get reads count on my chip seq reads

according to beedtools documentation site I've sorted and then indexed the bam file

bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed  <BED/GFF/VCF>

but i don't understand what does the bed file refer to ??

anybody who can help me, please?

thanks in advance

[GouthamAtla]

I want to use multicov mode to get reads count on my chip seq reads

Where do you want to measure the read counts ?

[rania.hamdy1]

i want to reads count histone modification in chip seq file REMC Dataset

[GouthamAtla]

The chip-seq data is usually represented as peaks of genomic coordinates in bed file format.

Answer 1

[ATpoint]

It is the intervals to quantify over (= your peaks) in BED format.

[rania.hamdy1]

I am a newbie in bioinformatic researches i can't understand your comment Can you explain more?

[ATpoint]

You really should get a solid background first. Check for example the vignette (the manual) of csaw which is a Bioconductor package to analyze ChIP-seq data. It offers a good introduction to ChIP-seq. Also spend time to get familiar with the common file formats (BED, BAM/SAM, GTF, FASTQ etc.). In this case the BED file is the template to count the reads so it is the parts of the genome that bedtools uses to count the reads. It does not automatically screen the entire genome but only the part you specify, e.g.:

chr1      1       450

would be an interval on chromosome 1 that could be a peak. Peaks come from peak calling. See e.g. the macs2 software package for peak calling.