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The tools — deepTools 3.4.3 documentation

Output format of plots should be indicated by the file ending, e.g. MyPlot.pdf will return a pdf file, MyPlot.png a png-file All tools that produce plots can also output the underlying data - this can be useful in cases where you don’t like the deepTools visualization, as you can then use the data matrices produced by deepTools with your favorite plotting tool, such as R

Deeptools.readthedocs.io

DA: 24 PA: 37 MOZ Rank: 61

Gallery of deepTools plots — deepTools 3.4.3 documentation

TATA box enrichments around the TSS of mouse genes ¶. Using the TRAP suite, we produced a bigWig file that contained TRAP scores for the well-known TATA box motif along the mouse genome. The TRAP score is a measure for the strength of a protein-DNA interaction at a given DNA sequence; the higher the score, the closer the motif is to the consensus motif sequence.

Deeptools.readthedocs.io

DA: 24 PA: 39 MOZ Rank: 64

General FAQ — deepTools 3.5.0 documentation

GenomeCoverageBed from the BEDtools suite can be used to calculate the number of bases in the genome for which 0 overlapping reads can be found. As described on the BEDtools website (go to genomeCov description), you need: a file with the chromosome sizes of your sample’s organism. a position-sorted BAM file.

Deeptools.readthedocs.io

DA: 24 PA: 33 MOZ Rank: 59

bamCoverage — deepTools 3.5.0 documentation

BamCoverage ¶. bamCoverage. If you are not familiar with BAM, bedGraph and bigWig formats, you can read up on that in our Glossary of NGS terms. This …

Deeptools.readthedocs.io

DA: 24 PA: 42 MOZ Rank: 69

computeMatrix — deepTools 3.5.0 documentation

ComputeMatrix. This tool calculates scores per genome regions and prepares an intermediate file that can be used with plotHeatmap and plotProfiles . …

Deeptools.readthedocs.io

DA: 24 PA: 44 MOZ Rank: 72

deepTools | Read the Docs

Stay Updated. Blog; Sign up for our newsletter to get our latest blog updates delivered to your inbox weekly.

Readthedocs.org

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DeepTools tutorial — HemTools latest documentation

Deeptools; scripting languange: Python; wiggle, bigwiggle or bedgraph format ¶ These file formats store signal values for each base, or a fixed/variable region. The simplest format will be bedgraph file, this is a 4-column tsv file and the columns are: chr, start, end, value; bigwiggle is just a binary format (compressed file) for bedgraph or wiggle. Wiggle format is little big …

Hemtools.readthedocs.io

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deeptools.getRatio — deepTools 3.5.0 documentation

Source code for deeptools.getRatio. import numpy as np old_settings = np. seterr (all = 'ignore')

Deeptools.readthedocs.io

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DeepTools — RCAC Biocontainers v1.0 documentation

RCAC Biocontainers latest Frequently Asked Questions. Frequently Asked Questions

Biocontainer-doc.readthedocs.io

DA: 31 PA: 42 MOZ Rank: 81

DEEPTOOLS COMPUTEMATRIX — Snakemake Wrappers …

DeepTools computeMatrix calculates scores per genomic region. The matrix file can be used as input for other tools or for the generation of a deepTools plotHeatmap or deepTools plotProfiles. For usage information about deepTools computeMatrix, please see the documentation. For more information about deepTools, also see the source code.

Snakemake-wrappers.readthedocs.io

DA: 33 PA: 48 MOZ Rank: 90

Main page — deepTools 0.0.1 documentation

DeepTools latest Stuff; BAR; deepTools. Docs » Main page; Edit on GitHub; Main page¶ blah blah blah ...

Dpryan79misc.readthedocs.io

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DEEPTOOLS PLOTPROFILE — Snakemake Wrappers tags/v1.6.0 …

DEEPTOOLS PLOTPROFILE¶. deepTools plotProfile plots scores over sets of genomic regions. As input, it requires a matrix file generated by deepToolscomputeMatrix.For usage information about deepTools plotProfile, please see the documentation.For more information about deepTools, also see the source code.. You can select which optional output files are …

Snakemake-wrappers.readthedocs.io

DA: 33 PA: 46 MOZ Rank: 90

Genome-wide profiling of histone H3K4me3 and H3K27me3 …

Schema for NTU-CAT. The schema for NTU-CAT is shown in Fig. 1.After removal of the zona pellucida, the embryos were immersed in a primary antibody solution containing a detergent (digitonin) and ...

Nature.com

DA: 14 PA: 28 MOZ Rank: 54

deepTools Documentation - Read the Docs

DeepTools consists of several command line and galaxy wrappers for summarising the information on Next Generation Sequencing data that can be mapped to a reference genome. However, the engine powering the deepTools commands can be used through the API for other purposes as well. The following is a short overview of the most useful methods and classes …

Media.readthedocs.org

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Deeptools on Biowulf - NIH HPC Systems

DeepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. deepTools offers multiple methods for highly-customizable data visualization that immensely aid hypothesis generation and data interpretation. It also offers all the tools needed to create ...

Hpc.nih.gov

DA: 11 PA: 20 MOZ Rank: 45

Blacklist Regions — deepTools 3.2.1 documentation

Using the –blackListFileName option available throughout deepTools. The subtraction of these regions is accounted for in all normalizations. Note. Some programs, such as bamCoverage, can use the number of reads in a file to estimate coverage for the purposes of normalization. Reads in blacklisted regions are subtracted for this purpose, but do note that the number of reads in …

Test-argparse-readoc.readthedocs.io

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Search — deepTools 3.2.1 documentation

Read the Docs v: latest . Versions latest Downloads On Read the Docs Project Home Builds Free document hosting provided by Read the Docs.Read the Docs.

Test-argparse-readoc.readthedocs.io

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HiCExplorer tools — HiCExplorer 3.7.2 documentation

Output format of plots should be indicated by the file ending, e.g. MyPlot.pdf will return a pdf file, MyPlot.png a png-file. Most of the tools that produce plots can also output the underlying data - this can be useful in cases where you don’t like the HiCExplorer visualization, as you can then use the data matrices produced by deepTools with your favorite plotting tool, such as R.

Hicexplorer.readthedocs.io

DA: 26 PA: 37 MOZ Rank: 80

Glossary of NGS terms — deepTools 3.2.1 documentation

For deepTools, the first 3 columns are important: chromosome, start position of the region, end position of the genome. do not confuse it with the bedGraph format (although they are related) example lines from a BED file of mouse genes (note that the start position is 0-based, the end-position 1-based, following UCSC conventions for BED files):

Test-argparse-readoc.readthedocs.io

DA: 35 PA: 37 MOZ Rank: 90

Common NGS data formats and tools — HemTools latest …

Tool: bedtools getfasta (aka fastaFromBed) Version: v2.30.0 Summary: Extract DNA sequences from a fasta file based on feature coordinates. Usage: bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> Options: -fi Input FASTA file -fo Output file (opt., default is STDOUT -bed BED/GFF/VCF file of ranges to extract from -fi -name Use the name field and coordinates for …

Hemtools.readthedocs.io

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