How to get strand information in the bed file of macs1.4 peak calling output?

Question

[harikrishnanc903]

I am new to MACS peak calling. I am not sure how to get the strand information in the bed output file after running macs tool. Using the strand information I need to extract the sequence from the genome. Any suggestion to add the strand information in the MACS output?

[Sej Modha]

ChIPSeq is not strand specific hence that information is not available in the MACS2 output. Please see @Devon Ryan's answer on this thread Why chip-seq is strand specific?

[harikrishnanc903]

Thanks. I have one more doubt. Homer does peak calling using the "findpeak".In homer output, we are getting strand information. Is it because homer uses a different algorithm to call the peak?

[ATpoint]

As said, there is no strand information from the biological side on ChIP-seq data. Ignore the strand, wherever this tools gets it from. Probably only counts reads from one strand or whatever.

Answer 1

[ATpoint]

There is no strand information, as ChIP-seq binding events are not strand-specific. DNA-binding factors and DNA-associated proteins, such as histones bind/are associated with double-stranded DNA. Why do you need the strand information, so what is your final goal?

[harikrishnanc903]

From macs output(bed file), I have contig start and end position. I will use this information to extract the sequence from the genome. I am concerned about whether we need the stand information in the bed file for doing the same.

[ATpoint]

You don't. Unless you have a good reason (getting a gene sequence), sequences are always extracted from the reference (= plus) strand.

Answer 2

[ZZzzzzhong]

Transcriptome usually comes from fixed chains.peak_result is your MACS out put and genes.gtf is your annotation file.

intersectBed -wo -a peak_result -b genes.gtf | awk -v OFS="\t" '{print $1,$2,$3,"*","*",$10}'|uniq > Peaks.bed
fastaFromBed -s -f genome.fa -bed Peaks.bed -fo Peaks.fa