how to combine individual chromosomal wig files into 1 bigwig file.

Question: how to combine individual chromosomal wig files into 1 bigwig file.

3.3 years ago by

hss • 20

United States

hss • 20 wrote:

I am using Galaxy on a PC. My peak calling software is a PC based program built into DNAstar. Unfortunately it does not have a way to concatenate the called peaks into a single bigwig file. The output is single chromosome specific wig files. Is there a way in the Galaxy wig to bigwig tool to have it combine multiple wig files into one bigwig file? I also do not have access to a Unix machine or a Mac. I did a test using EM editor and found that I can manually combine these files . I just need to re-enter by hand a line break b/w Chromosome track info. The files become huge and I am not sure that I can combine all the mouse chromosome wig files and still be allowed to upload it to Galaxy. Having a single bigwig file for all my called peaks will enable me to generate a single custom track in the USCS browser. I need to make six of these custom tracks to identify peaks where our molecule of interest is contacting the genome.

Thanks for everyone's thoughts on how to do this task.

concatinate wig galaxy bigwig • 1.6k views

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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by hss • 20

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool "Concatenate" can be used to merge datasets. The inputs will be one "stacked" on top of another.

Inserting blank lines between the chromosomes is not necessary to my knowledge. However, be certain to have only one browser line and one track line in the final result. A file of just a browser and track line can be loaded into Galaxy and then merged with the other data lines - just be sure to place this file at the top of the "stack" by entering it first on the tool form.

One declaration line per chromosome is still necessary (lines that start with "variableStep" or "fixedStep"). Do not mix types within a single dataset and do not combine more that one track in a single dataset.

Other tools for line manipulations (to strip off duplicate track lines and such), see the same tool group as the Concatenate tool: Text Manipulation.

At the very end, convert to bigWig, as this will be necessary for visualization at UCSC from Galaxy.

More about WIG/wiggle format specifications is here at UCSC: http://genome.ucsc.edu/goldenPath/help/wiggle.html

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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