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-   -   Wig File Formats (http://seqanswers.com/forums/showthread.php?t=5057)

Sanchari 05-10-2010 05:16 AM

Wig File Formats
 
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 05-10-2010 07:54 AM

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

Sanchari 05-10-2010 11:01 PM

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 05-20-2010 06:14 PM

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

Sanchari 05-20-2010 08:52 PM

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 05-20-2010 11:40 PM

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 05-20-2010 11:45 PM

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

john_mu 05-20-2010 11:47 PM

Quote:

Originally Posted by Sanchari (Post 18911)
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 05-21-2010 12:11 AM

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


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