How to create bigwig file in galaxy after MACS procedure(Chip Seq)
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16 months ago
anasjamshed ▴ 120

I have finished Chip Seq till MACS in Galaxy. galaxy

I want to get a bigwig file for motif detection. How can I do this?

ChIP-Seq Galaxy • 997 views
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While someone may answer here you may get prompt help at the Galaxy help forum: https://help.galaxyproject.org/

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Please stop adding bioinformatics as tags in your questions - every single post on this forum is related to bioinformatics - if not, they'd be marked off-topic and removed.

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16 months ago
Ian 6.0k

Hello.

A bigWig file is not suitable for motif detection, but can be viewed on, for example, UCSC genome browser or IGV, You will need a fasta sequence file, which you can obtain using the "summits in bed" output. You could use bedtools 'slop' or use Galaxy 'Compute' to add and subtract, e.g. 100bp from the end coordinate of the summit file. If you cut out the appropriate chr, start, end coordinates to a new file, you can then get the corresponding fasta sequence using 'Extract Genomic DNA'.

I hope this helps.

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What is the purpose of bigwig file then?

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Invest some effort and Google before you ask here. I googled "bigwig file" and the first link is: https://software.broadinstitute.org/software/igv/bigwig which says

The main advantage of the bigWig files is that only the portions of the files needed to display a particular region are transferred, so for large data sets bigWig is considerably faster than regular WIG files.

Also, following up on a previous discussion, are you a bioinformatician or a jeweller?

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