Search Results for "bedtools"

...Dependencies: python >= 2.7 version python packages: rpy2(v2.8.1), pysam(>0.8.4), pybedtools(v0.7.7) and wxpython (only for GUI form) R with following packages: gplots, ggplot2, RColorBrewer, FactoMineR, kernlab, bnlearn, igraph, fastcluster, caret and ROCR bedtools (2.16/2.17/2.25) Manual & different forms of EpiMINE can be downloaded is available under "Browse Files" section For any help, you can reach us at epimine.help@gmail.com

The script takes fastq files from sequence runs (or from bam files converted using bam2fastq) and aligns to a user-selected genome. Additional options to only convert reads above a certain mapping score, removing duplicates and generating bed files (requires Bedtools set in path).

A Java application to analyse Molecular Inversion Probe sequencing data within short time. Running the pipeline requires previous installation of three general tools: BWA, GATK and Bedtools. Input: For running the pipeline you need to specify 3 arguments. An example of the command is given below. The two input files are essential to specify the sample and run configuration. The environment argument should always be set to EMPTY. A brief description of other required files can be found in the example input files (see sampleConfigExample.txt and runConfigExample.txt). ...

User friendly program written in python and using bedtools to test for enrichment of GWAS SNPs in genomic annotation datasets. A specific feature is it tests for enrichment by locus not by individual SNPs. The user supplies 3 types of files. The first two files are a list of target SNPs and a list of background SNPs. To make the program user friendly the input format is simply the raw output from the popular haploreg program.

Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. usage ./fast_count_multi num_threads gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. ...

AnnotateGenomicRegions is a Java based web application that finds overlapping and/or neighboring genome annotations in a list of user-supplied genomic regions. As opposed to tools like CisGenome, BedTools, Bioconductor ChIPpeakAnno, or Galaxy, this tool is extremely easy to use and doesn't require downloading and installing software on the computer of the user nor any specific knowledge of the annotation software. Just copy and paste your regions or browse to a local text file containing your genomic regions. Several hundreds of thousands of genomic regions can be annotated with tens of known genome annotations at the same time. ...

BEDTools is a suite of utilities for comparing genomic features in BED format. These utilities allow one to quickly address tasks such as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps.