bedtools2 | bedtools - the swiss army knife | Genomics library

by arq5x C Version: v2.31.0 License: MIT

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | bedtools2 Summary

bedtools2 is a C library typically used in Artificial Intelligence, Genomics applications. bedtools2 has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

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Quality

Security

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Support

bedtools2 has a medium active ecosystem.

It has 825 star(s) with 280 fork(s). There are 57 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 196 open issues and 597 have been closed. On average issues are closed in 155 days. There are 20 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bedtools2 is v2.31.0

Quality

bedtools2 has 0 bugs and 0 code smells.

Security

bedtools2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

bedtools2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bedtools2 is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

bedtools2 releases are available to install and integrate.

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bedtools2 Key Features

No Key Features are available at this moment for bedtools2.

bedtools2 Examples and Code Snippets

No Code Snippets are available at this moment for bedtools2.

Community Discussions

Trending Discussions on bedtools2

Problems with bedtools installation

Combine shell command lines in snakemake

QUESTION

Problems with bedtools installation

Asked 2022-Mar-05 at 17:07

I am a very new beginner in bash programming and never succeed in installing tools on my computer.

I am trying to install bedtools without any success

I typed these following commands on my terminal

...

ANSWER

Answered 2022-Mar-05 at 17:07

It looks like you accidentally downloaded and compiled the program under your my_bin directory. That creates some potential for confusion, so I would recommend running the wget and make commands from a temporary directory, such as /tmp or a tmp directory under your home directory. As a result, the compiled binaries are now under /Users/avitrac/my_bin/bedtools2/bin. I would recommend moving that directory outside of your my_bin directory, perhaps to a ~/tmp directory; you could then skip directly to step 5 below.

(You could leave it there and simply cp /Users/avitrac/my_bin/bedtools2/bin/bedtools ~/my_bin, but that would leave the source code and compilation artifacts under your bin directory for no good reason).

mkdir ~/tmp ## if needed
cd ~/tmp
wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz
make
cp bin/bedtools ~/my_bin/

The bedtools-2.29.1.tar.gz file and bedtools2 directory can both be removed now. The "Compiling from source via Github" instructions gloss over this (fairly typical) use-case and omitted the explicit instructions to build the program in a temporary location.

Source https://stackoverflow.com/questions/71363705

QUESTION

Combine shell command lines in snakemake

Asked 2020-Feb-19 at 15:21

I would like to combine two command lines as one single to avoid the intermediate files.

...

ANSWER

Answered 2020-Feb-19 at 09:42

You probably get an invalid syntax because of the " you use in your shell here: Description="Gene name">. This closes your shell. You can either escape these quotes or use the """ syntax:

Source https://stackoverflow.com/questions/60297067

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install bedtools2

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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