Question: different BED Format for peak calling
0
gravatar for bxia
2.8 years ago by
bxia140
bxia140 wrote:

A little bit confused how it works, there are different types of BED format. When I used peak calling software, they should have different codes to deal with different format of BED?

I see there are Bed broadpeak, Bed narrowpeak, will I get different results when I pass these files from same sample to MACS2 and get different results?

chip-seq • 1.3k views
ADD COMMENTlink modified 2.8 years ago by greenelee0510 • written 2.8 years ago by bxia140
0
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

MACS2 expects BAM input and produces those formats as output.

ADD COMMENTlink written 2.8 years ago by Devon Ryan91k

Format of tag file, can be "ELAND", "BED", "ELANDMULTI", "ELANDEXPORT", "ELANDMULTIPET" (for pair-end tags), "SAM", "BAM", "BOWTIE", "BAMPE" or "BEDPE". Default is "AUTO" which will allow MACS to decide the format automatically. "AUTO" is also usefule when you combine different formats of files. Note that MACS can't detect "BAMPE" or "BEDPE" format with "AUTO", and you have to implicitly specify the format for "BAMPE" and "BEDPE".

The BED format can be found at UCSC genome browser website.

I think the BED is supported

ADD REPLYlink written 2.8 years ago by bxia140

Sure, but there's no reason to use ever use it, that's stuff largely predating the adoption of the BAM standard.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

Yeah, that is true, I am running it on my laptop, I am not sure differently download the BED file will save me some space and generate the same results.

ADD REPLYlink written 2.8 years ago by bxia140
1

You're better off taking the hit on space than trying to run MACS2 with BED files.

ADD REPLYlink written 2.8 years ago by Sinji2.8k
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