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4 votes
Accepted

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
  • 19.6k
4 votes
Accepted

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
Accepted

Dealing with absence of coverage

I'll fix the bamCoverage issue in the 2.6.0 release (it may already be fixed since I rewrite how bigWig files are made for that release). You can follow my status ...
Devon Ryan's user avatar
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3 votes

Clarification regarding (deepTools) bamCoverage output

Yes The total RPKM for the region in the bedgraph file is the value already present in the bedgraph file. If you want to estimate the RPKM for a larger region composed of multiple bins then you can ...
Devon Ryan's user avatar
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2 votes

Error while running computeMatrix command in Deeptools

It worked, I installed a the newer version of deeptools, from GitHub: https://github.com/deeptools/deepTools
1 vote

Warning message related to tensorflow package when trying to run deepbgc bioinformatics tool

The 'blunderbus' way to do this is as follows (not recommended in this instance :-) ), ...
M__'s user avatar
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1 vote

pip installation within conda env: Error downgrading scikit-learn - WARNING: No metadata

pip and conda don't mix and good advice is don't ever mix them. Thus to avoid this delete your old environment, create a new <...
M__'s user avatar
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1 vote
Accepted

How to calculate the number of peaks that are upstream/downstream of some other peaks

You can use windowBed from bedtools with -c if you just want counts. Or use -wa -wb and then ...
geek_y's user avatar
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1 vote
Accepted

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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1 vote

merge the matrix from computematrix of deeptools

You're trying to cbind two matrices of different sizes, so computeMatrix is throwing an error since it's unclear which row goes with which. You need to ensure that matrices have exactly the same ...
Devon Ryan's user avatar
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1 vote

plot correlation between several bam files

That's a completely normal way to plot correlation between them. Spearman correlation was a wise choice on your part, since it's rank based and you don't have to care as much about normalization. ...
Devon Ryan's user avatar
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1 vote
Accepted

Pol_II genome wide occupancy analysis

comment discussion between @krushnach-chandra and @stupidwolf (in chronical order): SW: No you don't need gene expression data.. You can just count the reads from polII chip (normalized by some method ...
1 vote
Accepted

multiBamSummary output chromosome region annotate issue

Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.
Devon Ryan's user avatar
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1 vote

Different outputs of computeMatrix depending on binsize

Please don't send things like this to the deepTools mailing list and post them here. As I mentioned on the list, what you're likely being surprised by is that computeMatrix is not summing values, but ...
Devon Ryan's user avatar
  • 19.6k

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