Results for "command"
Blogs
How to install Perl modules manually, using CPAN command, and other quick ways
...l Perl modules using CPAN, make sure the cpan command is working. Following are the...AN module is not installed.# cpan-bash: cpan: command not found# perl -MCPAN -e she...)? [ask]Parameters for the 'perl Makefile.PL' command? []Parameters for the 'perl B...4001 days ago
- ...may be in a slightly different location. The commands below show where they were o...file (save the patch into a file and use the command patch < patchfile.)Then, r...toryThis was fixed with the following apt-get command (in the bash shell)$ sudo apt...
3991 days ago
- +17 more Blogs
Bookmarks
Taverna Workflow Management System
...rna Workbench(the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick executi...3967 days ago
- ...on tools:* CuffDiff* EdgeR* DESeq2 Advanced Command Line Tutorial Graphical Output with CummeRbund introduces some basic commands using the cummeRbund package...those who are comfortable with using the UNIX command line; and often allow more co...
3704 days ago
- +65 more Bookmarks
Files
Detect the sequence pattern and its location in fasta file with match and mismatches information.
This script is one of my old script to detect some centromeric pattern in chromosomes. User can also control the number of mismatches allowed through command line .. To run: perl centro.pl3919 days ago
- Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3918 days ago
Pages
Bio++ : C Language libraries for your biological need
...rt text to any other type and vice versa, remove spaces, tokenize, switch between upper/lower case, etc.Applications: read options from a file or command lineetc. Some of the librari...3999 days ago
- ...mputer and visa-versa. I am jotting down some of the commonly used SCP command for your future help. Hope yo...to increase speed. This can be done by using option -c blowfish in the command line. $ scp...
3753 days ago
- +13 more Pages
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...or, BMC Bioinformatics 11(Suppl 12):S1, 2010 Full Text Links to Linux command-line tutorials and resources...e Barnett's awk tutorial Greg Goebel's awk tutorial Executing an awk command from R to simplify data explo...3831 days ago
List of In-silico Binding Site Prediction Tools
...n pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program. A GUI is...3795 days ago
- +23 more Top-level pages
Wire posts
News
Linux operating system aimed at scientists
...Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just...3445 days ago
- ...-alikes.) system(cmd, input = ) now uses ‘shell-execution-environment’ redirection, which will be more natural if cmd is not a single command (but requires a POSIX-complia...
3357 days ago
Opportunity posts
Internship in Computational Biology
...rmal applications are due by Sunday 2nd December 2012. Requirements: This position requires a good understanding of genetic problems, a good command of at least one scripting lan...3583 days ago
JRF Bioinformatics at National Institute of High Security Animal Diseases (ICAR)
...ipline). Desirable : Exposure of working in research environment, Good command over written/spoken English a...ed areas. Desirable: Exposure of working in research environment, Good command over written/type written/spo...3347 days ago
- +5 more Opportunity posts
Fun
- ...the inheritance! Why did bioinformatician always works on the command line? A: Because they don't...; fsck; fsck; umount; clean; sleep; A: Ah, Ohhh, dude, these are *NIX commands Did they really hac...
3232 days ago
Video
Bioinformatics 101 - Running BLAST
How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at t...3948 days ago
- Presented July 30, 2014 and covering: an NCBI BLAST AMI at Amazon Web Services; introduction to AWS and setting up an instance; running command line BLAST and using the BLAST URL API via the AMI; and answers to attendee questions.
3571 days ago
Bio-Scripts
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003...1153 days ago
R script to visualize fastANI core-genome comparison
...e comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_fasta=c...1153 days ago
- +58 more Bio-Scripts
Tags
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam ...Tags: Frequent, Paired-end, reads, (PE 2x100), mapping, command, lines
2233 days ago
Comments
Comment on "Benchmarking Perl Module !"
...hmark module: Install the Benchmark module: If you don't already have the Benchmark module installed, you can install it using the following command: cpan Benchmark Write b...467 days ago
Comment on "Short-read assembly using Spades !"
...ic or FastQC. Running SPAdes: After quality control, the next step is to run SPAdes. This can be done through a command-line interface or a graphical user interface. The command for running SPAdes is usually...467 days ago
- +29 more Comments
