Results for "data compression"
Bio-Scripts
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...1553 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/...w be installed into this location: /data/sata_data/workshop/wsu29/anaconda3...y37_0 ... installing: importlib_metadata-0.8-py37_0 ... installing: j...py37_0 ... installing: pytest-remotedata-0.3.1-...1550 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/sata_d...1550 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 (repod...1550 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...1550 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...1544 days ago
- (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata.json):...
1540 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get the...| grep SRR | head -$N > selected.txt # Store the data in the...1536 days ago
- $MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot [sudo] p...led: aglfn gnuplot gnuplot-data gnuplot-qt libdouble-conversi...bionic/universe amd64 gnuplot-data all 5.2.2+dfsg1-2ubuntu1 [56....-conversion1:amd64. (Reading database ... 189871 files and dire...sg-3) ... Setting up gnuplot-data (5.2.2...
1535 days ago
Install python-numpy python-scipy python-matplotlib on Ubuntu !
$MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-...ecorator python-matplotlib-data python-olefile python-pil pyt...-matplotlib python-matplotlib-data python-numpy python-olefile p...verse amd64 python-matplotlib-data all 2.1.1-2ubuntu3 [3,774 kB]...ted package python-matplotlib-data. Prep...1535 days ago
