BOL

The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads...

samtools index your.bamsamtools view your.bam "chr5:200-6000" > output.bam That would output all reads in chr5 between 200-6000 bp.

 I want to extract all the reads mapped at chr5: 200-6000. 

Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which...

MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by selecting the type of identifier...

Learn D3.js - https://leanpub.com/D3-Tips-and-Tricks/read #D3dotJS #visualisation #plot

Writing is more effective way to learn than reading. While writing you get more information and hence can improve your personal skills and knowledge. Every student likes to get a good essay, for getting good essay students must follow the some...

To do sam to bam conversion, follow the following commands :-  Code: $ samtools view -b -S file.sam > file.bam Then you will need to use  Code: $ samtools sort file.bam file-sorted followed by Code: $ samtools index...

There are common options for most BBMap suite programs and depending on the file extension the input/output format is automatically chosen/set.Note: For most programs in BBTools, you can add the parameter "config=foo.txt". Every line in...

RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can...

urbe@urbo214b[genome] graphmap align -h []GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapperGraphMap Version: v0.5.2Build date: Jun 6 2017 at 15:45:57 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan...

Transposons or Transposable elements (TEs) are "mobile genes" capable of mobilization from one genomic location to another through non-homologous recombination. As this movement is mediated by its own proteins and does not contribute to the survival...

PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...

samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam

The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfred dependencies are included as submodules so you need to do a recursive...

Bioinformatics jobs at http://svimsbic.org/SRF_Notification.pdf #SVIMSBIC #Bioinformatics