Results for "Data Mining & Statistical Study"
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 SRR17704...he only major change from bwa mem is that we'll tell it we're working with short read data...1572 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl...will now be installed into this location: /data/sata_data/...1.0.1-py37_0 ... installing: importlib_metadata-0.8-py...-0.3.2-py37_0 ... installing: pytest-remotedata-...1568 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/min...Miniconda3 will now be installed into this location: /data/sata_data/worksh...running conda init? [yes|no] [no] >>> yes no change /data/...1568 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done...ckage Plan ## environment location: /data/...install samtools Collecting package metadata (repod...da install picard Collecting package metadata...1568 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 environment...n ## environment location: /data/s...96ca727_0 193 KB r-gdata-...-fansi-0.4.0-r36h96ca727_0 r-gdata...#################### | 100% r-gdata-...1568 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [s...ight (C) 2018 The R Foundation for Statis...cking for local ICUDT_DIR... icu61/data...... no checking for available ICU data library (ucnv, uloc, utrans)... yes...4-linux-gnu -licui18n -licuuc -licudata...1563 days ago
- (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata....
1559 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...rep SRR | head -$N > selected.txt # Store the data...1555 days ago
- $MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot [sudo] pas...be installed: aglfn gnuplot-data gnuplot-qt libdouble-conversi...alled: aglfn gnuplot gnuplot-data g...u bionic/universe amd64 gnuplot-data...le-conversion1:amd64. (Reading database .....dfsg-3) ... Setting up gnuplot-data...
1554 days ago
Install python-numpy python-scipy python-matplotlib on Ubuntu !
$MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-scipy py...python-decorator python-matplotlib-data p...python-matplotlib python-matplotlib-data...onic/universe amd64 python-matplotlib-data all 2....unselected package python-matplotlib-data....1554 days ago
