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How to convert BAM file to bigWig in Python?

deepTools has a (somewhat poorly documented) API, since it's a python package too. The basic code framework is: ...
Devon Ryan's user avatar
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4 votes
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Customizing bigWig file

There's no equivalent to the wiggle header in bigWig (or bigBed) files, which is why UCSC uses the file name. This is actually the reason for the track line stuff that you linked to, since you can ...
Devon Ryan's user avatar
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4 votes
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What unit do I get on the y-axis of a metagene profile plot?

Feel free to @ me in deepTools questions, since I'm the primary developer. For a given bin, the count assigned to it is the number of reads overlapping it, regardless of whether they overlap by 1 or ...
Devon Ryan's user avatar
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3 votes

How to convert BAM file to bigWig in Python?

pyranges: import pyranges as pr gr = pr.read_bam("your_file.bam") gr.to_bigwig("out.bw", chromosome_sizes=pr.data.chromsizes()) # for hg19
The Unfun Cat's user avatar
3 votes
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Adding entries to bigwig file

Presuming you still have your BAM file sitting around somewhere: ...
Devon Ryan's user avatar
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2 votes

Is there a standard method to validate whether a bigWig file is correct?

There's no standard validation method, but a simple one would be python -c "import pyBigWig; bw = pyBigWig.open('your_file.bw'); print(bw.IsBigWig());". If you get <...
Devon Ryan's user avatar
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2 votes

BigWig circular plot representation

circosJS should probably work well, based on your requirements: https://github.com/nicgirault/circosJS I posted a short Observable notebook that shows what calls could be used to bring data from ...
Alex Reynolds's user avatar
2 votes
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Time and memory efficient processing of many intervals for a bigWig file

Assuming you can make a BED file of introns, you can then use the pyBigWig module in python: ...
Devon Ryan's user avatar
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1 vote

RNA seq .counts.txt to bigwig conversion

No, count-level data doesn't have the base-level resolution that is required in order to be usefully visualised on a genome browser. You need a BAM file (or raw FASTQ files that can be used to ...
gringer's user avatar
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1 vote
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Is there a standard method to validate whether a bigWig file is correct?

As noted in another answer, it's relatively easy to tell if a file is bigWig or not by opening it up with, say, standard UCSC Kent utilities like bigWigToBedGraph ...
Alex Reynolds's user avatar
1 vote

bigWig to bed for regions above/below threshold

Convert bigWig to WIG via bigWigToWig: $ bigWigToWig signal.bw signal.wig Convert WIG to BED via BEDOPS ...
Alex Reynolds's user avatar
1 vote
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bigWig to bed for regions above/below threshold

You can do that with a bit of python: ...
Devon Ryan's user avatar
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1 vote
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IGV faster loading remote bigWig files

You would need to do this when creating the bigWig file. Note that I'm not aware of anything that allows manually setting the various zoom levels (libBigWig/pyBigWig will allow you to set a max number,...
Devon Ryan's user avatar
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