Results for "data visualization"
Bio-Scripts
$ sudo apt install npm Reading package lists... Done Building...node-forever-agent node-form-data node-fs.realpath node-fstr...onic/universe amd64 node-form-data all 0.1.0-1 [6,412 B]...amd64 node-normalize-package-data all 2.3.5-2 [10.6 kB]...ackage node-normalize-package-data. Prepar...1551 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) {...ine; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ apple...1559 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fas...he SRA toolkit. It allows directly downloading data from a particular sequencing...q-dump --split-files SRR1770413 #SRA stores data in a par...1558 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 SRR1770413_2.fastq.gz \...major change from bwa mem is that we'll tell it we're working with short read data using -a...1558 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/...be installed into this location: /data/sata_data/workshop/wsu29/anaconda3...37_0 ... installing: importlib_metadata-0.8-py37_0 ... installing: j...y37_0 ... installing: pytest-remotedata-0.3.1-py...1554 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-...nda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3...nda init? [yes|no] [no] >>> yes no change /data/sata_dat...1554 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environme...## environment location: /data/sata_data/workshop/wsu29/anac...mtools Collecting package metadata (repodata.json): done Solvin...picard Collecting package metadata (repodat...1554 days ago
Bash command to install GATK, Bedtools and SnpEff !
(my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata (repodata.json): done Solving environm...a727_0 193 KB r-gdata-2.18.0 | r36h6...nsi-0.4.0-r36h96ca727_0 r-gdata pkgs/r/noarch::r-g...################# | 100% r-gdata-2.18.0...1554 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo...checking for local ICUDT_DIR... icu61/data checking for gcc... gcc -std...set... no checking for available ICU data library (ucnv, uloc, utrans)....6_64-linux-gnu -licui18n -licuuc -licudata -L/usr/l...1548 days ago
- (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata.json): d...
1545 days ago
