I am working on a project and I'm trying to find data on the position of genes and heterochromatin binding sites such as HP1 in Drosophila melanogaster. Is this information available for the DGRP lines? Would I be able to measure the distance between a gene and its nearest binding site from such data?
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2 Answers
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Have a look at these ChIP-seq data for HP1 in Drosophila: 1, 2 and 3. From ChIP-seq data you can find the distance between the TFBS peaks and the TSS of the gene.
You can also look for nucleosome positioning and DNAse hypersensitvity regions; for the former, I am sure that data is available for Drosophila.
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As the previous answer said, there are some public HP1 ChIP-seq data from D. melanogaster if not from the DGRP, from modENCODE and maybe others. In the case of modENCODE, they've published not only the reads, but also their peak calls (mapping with Eland + calling with MACS).
BEDTools ( https://github.com/arq5x/bedtools2 )is a nice command line tool for manipulating intervals with genomic coordinates, and the bedtools closest command can calculate the distance to the closest feature. It would look something like this:
bedtools closest -d -a genomic_features.gff3 -b peak_calls.gff3
Where the "genomic_features" part would be any subset of genome annotation that you're interested in.
I've worked through a small example with modENCODE data, Flybase transcript annotation and BEDTools:
http://martinsbioblogg.wordpress.com/2014/07/04/finding-the-distance-from-chip-signals-to-genes/
Cheers,
m.
