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I am working with custom fasta and custom bedgraph files so that my bedgraph file looks like the following:
```
BarcodeRep-TSS-chr10:92593086-92593236,+ 1 1 0.0
BarcodeRep-TSS-…
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The prebuild statistics are part of the genomic resource files. For example, for a position score `phyloP7way,` the directory structure should be similar to the following:
```
phyloP7way/
├── genomic_…
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Hi,
I have access to bigWig file from an ATACseq experiment, but I do not have the original fastqs nor the bam files of the alignment. I wanted to know if there is a way to identify peaks from thi…
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I install `macs2` using `conda` and `which` can find it, but MACS2 throws errors when I try to run it about not being able to find files.
```
balter@server:~$ conda install macs2
Fetching package met…
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`BedTool.genome_coverage` sometimes returns bedGraph-like output, sometimes not. In fact, by default, it doesn't return a valid BED-ish format file.
See #110, #111, #112.
_note to future self: this…
daler updated
4 years ago
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Hi all,
- I ran CUT&RUN experiments with 200.000 cells per experiment and H3K27me3 (CST #9733 antibody) being my positive control and IgG being my negative control.
- These were all sequenced at…
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![2023-10-27 - 15-52-34 - PlasmoDB -- JBrowse](https://github.com/elsiklab/multibigwig/assets/39096257/dabb1426-7b00-4e43-812b-6615d7c6b9cb)
The image above shows individual XY tracks and a multi…
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When running `macs2 callpeak` with the flags `-g GSIZE -B --SPMR` are the bedGraphs files produced normalised to reads per million (RPM), or is the effective genome size included in the calculation (…
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Hi,
I tried peak calling for a transcription factor with two IgG control files (test & control was spiked with E.coli DNA and normalized with scaling factor as described in protocols.io data proce…
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Hi after running ORFquant i got all the expected output files ex. gtf file, fasta file, final results file and tmp file but pdf/html reports not produced.
When i tried producing using the ORFquant …