Question

GC content of promoters

1

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10.7 years ago

asharmatelome ▴ 60

I have a file from Chip-Seq data. I want to use this information to look for the GC content of promoters.

Which software I can use?

Thanks
Ankur

GC ChIP-Seq genome • 3.3k views

ADD COMMENT • link updated 3.4 years ago by Ram 44k • written 10.7 years ago by asharmatelome ▴ 60

Ram · Accepted Answer · 2014-05-22

3

Entering edit mode

10.7 years ago

aditi.qamra ▴ 270

The simplest would be to use nuc option in bedtools.

bedtools nuc -fi $ref-fasta-file -bed $promoterbedfile > $outputfile

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ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 10.7 years ago by aditi.qamra ▴ 270