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bedtools — Janis documentation
BEDTools: coverageBed bedtoolsCoverageBed (1 versions) v2.29.2. BEDTools: genomeCoverageBed bedtoolsgenomeCoverageBed (1 versions) v2.29.2. BEDTools: intersectBed bedtoolsintersectBed (1 versions) v2.29.2. Revision e1ae6b21. Built with Sphinx using a theme provided by Read the Docs. Read the Docs v: latest Versions latest stable …
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bedtools | Read the Docs
Stay Updated. Blog; Sign up for our newsletter to get our latest blog updates delivered to your inbox weekly.
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bamtobed — bedtools 2.29.0 documentation
BamToBed [OPTIONS] -i <BAM>. Option. Description. -seq. Write sequence addtional to bed6. -bedpe. Write BAM alignments in BEDPE format. Only one alignment from paired-end reads will be reported. Specifically, it each mate is aligned to the same chromosome, the BAM alignment reported will be the one where the BAM insert size is greater than zero.
My-bedtools2.readthedocs.ioDA: 27 PA: 38 MOZ Rank: 67
getfasta — bedtools 2.29.0 documentation
Tip. 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.. 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold-w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing. 3. BED files containing a single region require a newline character at the end of the …
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BEDTools: coverageBed — Janis documentation
BEDTools: coverageBed¶ bedtoolsCoverageBed · 1 contributor · 1 version. The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a ...
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BEDTOOLS — Snakemake Wrappers tags/v1.6.0 documentation
BEDTOOLS¶. For bedtools, the following wrappers are available: BEDTOOLS COMPLEMENT; COVERAGEBED; BEDTOOLS GENOMECOVERAGEBED; BEDTOOLS INTERSECT
Snakemake-wrappers.readthedocs.ioDA: 33 PA: 33 MOZ Rank: 71
BEDTOOLS INTERSECT — Snakemake Wrappers tags/v1.6.0 …
Note that input, output and log file paths can be chosen freely. When running with
Snakemake-wrappers.readthedocs.ioDA: 33 PA: 43 MOZ Rank: 82
BEDTOOLS SORT — Snakemake Wrappers tags/v1.0.0 …
BEDTOOLS SORT¶. Sorts bed, vcf or gff files by chromosome and other criteria, for more information please see bedtools sort documentation.. URL:
Snakemake-wrappers.readthedocs.ioDA: 33 PA: 38 MOZ Rank: 78
BEDTools: genomeCoverageBed — Janis documentation
BEDTools: genomeCoverageBed¶ bedtoolsgenomeCoverageBed · 1 contributor · 1 version. bedtools genomecov computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. Note: 1. If using BED/GFF/VCF, the input (-i) file must be grouped by chromosome. A simple ...
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BEDTOOLS GENOMECOVERAGEBED - snakemake …
BEDTOOLS GENOMECOVERAGEBED¶ bedtools ’s genomeCoverageBed computes the coverage of a feature file as histograms, per-base reports or BEDGRAPH summaries among a given genome. For usage information about genomeCoverageBed, please see bedtools ’s documentation. For more information about bedtools, also see the source code.
Snakemake-wrappers.readthedocs.ioDA: 33 PA: 43 MOZ Rank: 85
Bedtools — Sheffield HPC Documentation
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.} module-whatis {Homepage: https://bedtools.readthedocs.io/} module-whatis {URL: https://bedtools.readthedocs.io/} set …
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Plot Venn diagram given two bed files - Read the Docs
This program will calculate the amount of overlaps given two bed files. Note that, it is very likely that the number of A overlapping with B is different than the number of B overlapping with A. For example, let’s say A is an entire chromosome, B is some scattered regions in this chromosome.
Hemtools.readthedocs.ioDA: 23 PA: 46 MOZ Rank: 80
getfasta — bedtools 2.25.0 documentation
Tip. 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.. 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold-w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing. 3. BED files containing a single region require a newline character at the end of the …
Teaching.readthedocs.ioDA: 23 PA: 38 MOZ Rank: 73
The tools — deepTools 3.5.0 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.ioDA: 24 PA: 38 MOZ Rank: 75
Building a Dataset Exon Database for BEDTools # - AltAnalyze
With this utility, you will instruct BEDTools to extract read counts for exon coordinates in your BAMtoBED exon database from AltAnalyze. Example instructions are shown here. Re-run AltAnalyze. Once the exon-level BED files have been produced, save these to the same folder as your junction.bed files. The junction and exon files will need to have the same beginning …
Altanalyze.readthedocs.ioDA: 25 PA: 20 MOZ Rank: 59
bedtools - protocols.hostmicrobe.org
Bedtools is a powerful toolset for genome arithmetic. Version: v2.26.0 About: developed in the quinlanlab.org and by many contributors worldwide. Docs: http ...
Protocols.hostmicrobe.orgDA: 25 PA: 44 MOZ Rank: 84
BedtoolsCoverageToCounts - Biopet User Manual
Input: A coverage file produced with bedtools output: A count file with the counts from the the values inside the coverage file. Where values could be almost everything, e.g. genes, ensemblIDs etc. etc. To run the tool: biopet tool BedtoolsCoverageToCounts Next Previous. Built with MkDocs using a theme provided by Read the Docs. Read the Docs ...
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Docker Hub
Docker Pull Command. Source Repository. Github. dceoy/docker-bio. Why Docker. Overview What is a Container. Products. Product Overview. Product Offerings
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bedtools/2.26 — Research Computing Center Manual
bedtools/2.26¶ name bedtools version 2.26.0 description Bedtools is a fast, flexible toolset for genome arithmetic. url https://bedtools.readthedocs.io license opensource built Thu Apr 6 22:20:27 CDT 2017 tags genetics, genomics usage Use the module system to load this version of bedtools: module load midway2; module load bedtools/2.26
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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 …
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