Wig File Formats

[Sanchari]

Hello,
I am having problems regarding wig files. I wanted to know the names/accession numbers of genes having certain histone modifications. Most papers are genome wide having chip-on-chip information and they give the supplementary information in wig files. I am unable to interpret the files. Need help regarding this issue .....

[yjhua2110]

please see UCSC website: http://www.genome.ucsc.edu/goldenPath/help/wiggle.html

[Sanchari]

Thanks for the link. I have pasted the first few entries in the wig file and this is how it looks. I viewed it in the UCSC genome browser. I am confused regarding the cut off I should be taking...do I have to consider the regions having 1 or 2 as entries...
Kindly reply...

track type=wiggle_0 name="GMAT_H3K9K14ac2" description="GMAT_H3K9K14ac2_hg18" visibility=full autoScale=off viewLimits=0.0:15.0 color=0,0,0

variableStep chrom=chr1 span=21

554973 1

554990 3

556480 1

559247 2

559431 2
.........etc

[john_mu]

What do you see in UCSC browser that you are not expecting?

[Sanchari]

UCSC will show the peaks for histone modifications for sure....but I wanted to know the specific list of genes whose promoters are having those modifications.....my wig file contains a huge number of chromosomal locations and I wanted to know which of these are coinciding with gene promoters....

[john_mu]

Sorry, I'm not too familiar with the display of histone modifications, so I can't help you there.

But, I'm guessing you are looking for a way to find gene annotations which are close to significant peaks automatically?

[Sanchari]

Yea...ur right..I need the gene names having significant peaks...

[john_mu]

Yea...ur right..I need the gene names having significant peaks...

hmm... I'm not aware of an automatic way of doing that. However, it is possible to download the annotations as a text file. Maybe you can write a short script to search through them based on the location of the peaks in the wig file.

[Sanchari]

yea...ok....I'll have to write some scripts to map the annotation data to the wig file..