Results for "NGS data analysis"
Bio-Scripts
Setting up falconUnzip conda environments for genome assembly !
...$ conda deactivate ➜ Analysis_Results source activate denovo_asm (denovo_asm) ➜ Analysis_Results conda install pb-asse...e currently available SMRT(R) Analysis builds. While # # efforts ha...e currently available SMRT(R) Analysis builds. While # # efforts ha...1982 days ago
- $ 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. P...
1545 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) { #prin...ne; } continue { $_ = $next_line; } print $_ if eof; } __DATA__...1552 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...it. It allows directly downloading data from a particular sequencing...it-files SRR1770413 #SRA stores data in a particular compressed fo...tools, so it's necessary to put things into...1551 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 usi...1551 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd...stalled into this location: /data/sata_data/workshop/wsu29/anaconda3...7_0 ... installing: webencodings-0.5.1-py37_1 ... installing:..... installing: importlib_metadata-0.8-py37_0 ... installing: j...1547 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-l...onda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3...onda init? [yes|no] [no] >>> yes no change /data/sat...1547 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environmen...## environment location: /data/sata_data/workshop/wsu29/anac...amtools Collecting package metadata (repodata.json): done Solvin...picard Collecting package metadata (re...1547 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-2.1...1547 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...for local ICUDT_DIR... icu61/data checking for gcc... gcc -st...o checking for available ICU data library (ucnv, uloc, utrans)....cudata *** compiler settings used: CC=gcc -std=gnu99...tri_exception.o stri_ICU_settings.o stri_join.o stri_length.o st...ux-gnu -licui18n -licuuc -licudata -L/...1542 days ago
