Results for "Javascript; Database: MySQL; Microarray data Analysis; Comparative Genomics; NGS; Proteomics; Molecular Phylogenetics; Teaching"
Bio-Scripts
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Proc...1998 days ago
- $ sudo apt install npm Reading package li...m node-forever-agent node-form-data n...de-nopt node-normalize-package-data...m node-forever-agent node-form-data nod...ionic/universe amd64 node-form-data all...e amd64 node-normalize-package-data all 2.3.5...package node-normalize-package-data. P...
1561 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = )...xt_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__...1569 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from...is in the SRA toolkit. It allows directly downloading data from a pa...fastq-dump --split-files SRR1770413 #SRA stores data in...1568 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR177041...only major change from bwa mem is that we'll tell it we're working with short read data usi...1568 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkd...3 will now be installed into this location: /data/sata_data/work...b-1.0.1-py37_0 ... installing: importlib_metadata-0.8-py37_...es-0.3.2-py37_0 ... installing: pytest-remotedata-0.3...1564 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/minico...Miniconda3 will now be installed into this location: /data/sata_data/workshop/...nning conda init? [yes|no] [no] >>> yes no change /data/sat...1564 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json):...e Plan ## environment location: /data/sata...tall samtools Collecting package metadata (repodata...nstall picard Collecting package metadata (re...1564 days ago
Bash command to install GATK, Bedtools and SnpEff !
(my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata (repodata...an ## environment location: /data/sata_d...h96ca727_0 193 KB r-gdata-2.18...r-fansi-0.4.0-r36h96ca727_0 r-gdata...##################### | 100% r-gdata-2.1...1564 days ago
Install Nucmer on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install mummer [sudo] password for jit:...1,213 kB in 2s (672 kB/s) Selecting previously unselected package gawk. (Reading database...1558 days ago
