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Old 06-15-2015, 10:10 AM   #1
yu_chem
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Location: Japan

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Default How to give peaks data of ChIP-seq annotation

Hi everyone

I want to ask you how to give peaks data of ChIP-seq annotation.
For understanding peaks data generated by MACS as bed file or xls file of peaks, I want to know What genes including each peak or Which peaks were included in intergene.
However I'm beginner of bioinformatic analysis and don't have a teacher of bioinformatician in my lab.

What software should I use? or What should I learn?
Sorry that I don't have knowledge enough...
For analysis, I use linux

Thanks in advance
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Old 06-16-2015, 12:24 AM   #2
SylvainL
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I guess you have an annotations file... so you can easily have a bed file with the gene coordinates.

You can either use intersectBed from bedtools (option -v to have non overlapping regions).

Or with R and the package Rsamtools, you can use the functions setdiff, intersect, findOverlaps... (just keeping in mind you want first to have a GRanges object of your intergnic regions first, which you will have to make).

s.
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Old 06-18-2015, 03:41 AM   #3
yu_chem
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Thank you for answer.
Sorry that I have not studied enough.

On the basis of your hint, I will study more
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