wig files beyond chromosome coordinates

[Venu]

Hi MACS users

I am using MACS version 1.4.0rc2. Sometimes the coordinates in the wig
files generated are beyond the coordinates of actual chromosome size.
I am sure I have seen a post regarding this which suggests to replace
the script with an updated one. I am now unable to find it. The only
thing I could see is dealing with negative coordinates in bedgraph
file. Can someone please tell me which program I need to update to
avoid this happening. Thank you very much for your help.

Venu

[Tao Liu]

Hi Venu,

Nowadays, I like to convert wiggle or bedGraph to bigwig. So if you want to do so, "wigToBigWig -clip foo.wig chromosome.txt foo.bw" can clip out the values outside of chromosome boundaries and convert wig file to bigwig. BigWig is more convenient for visualization on UCSC browser or IGV. And our Cistrome team is developing tools for bigwig files based on James Taylor's bx-python where he implemented some python wrappers for UCSC toolkits. Download wigToBigWig here: http://hgdownload.cse.ucsc.edu/admin/exe/. And the chromosome size file can be downloaded in UCSC download page <http://hgdownload.cse.ucsc.edu/downloads.html>, for example <http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>

HTH,

Tao

[Venu Pullabhatla]

Hi Tao

Thank you very much for your suggestion.

Venu

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Venu Pullabhatla, Ph.D.
Bioinformatician
NIHR GSTFT/KCL Comprehensive Biomedical Research Centre
Guy's & St. Thomas' NHS Foundation Trust
8th Floor, Tower Wing, Guy's Hospital
Great Maze Pond, London SE1 9RT