How to open/work with wig or tdf files

Question

[Apex92]

Hi all,

I have downloaded ChIP-seq data from a publication in .wig format to look at the chromatin mark signals in IGV. The recommendation of IGV is to convert .wig files to .tdf format for faster performance.

My question is that how can I work on these .tdf or wig files using bash or python? I would like to transform the signals from these files into numerical values for each gene in order to perform some calculations.

Any recommendation is appreciated. Thank you.

[cmdcolin]

you can use wigToBigWig command line too to make it a bigwig file. this would probably get similar performance as tdf

Answer 1

[jared.andrews07]

I'd advice against trying to analyze already processed wig files unless you're very sure they show what you expect. The data may have been transformed, normalized, or otherwise altered such that additional analysis may not be appropriate in the way that you'd hope.

If you really wanted to proceed, you could convert the wig to a BED file via bedops, and then pull values for your genic regions via bedtools or bedops followed by summing the values across each gene. Or something similar depending on what you're trying to actually do.

[Apex92]

Thank you Jared for your answer, it helped a lot. I do not do involved analyses on the wig files but just want to have the peak values for genomic locations so that I can make plots for better comparison and interpretation.