Results for "data"
Bio-Scripts
Bash script to alignment of short reads against reference genome !
...SRR341549.raw.sorted.minimap2.bam SRR341549.minimap2.bam #The only major change from bwa mem is that we'll tell it we're working with short read data using -ax sr:1557 days ago
Bash commandline to install Anaconda !
...3 will now be installed into this location: /data/sata_data/workshop/wsu29/anaconda3...b-1.0.1-py37_0 ... installing: importlib_metadata-0.8-py37_0 ... installing: j...es-0.3.2-py37_0 ... installing: pytest-remotedata-0.3.1-py37_0 ... installing:...1553 days ago
Bash command to install Miniconda !
...:' >>> yes Miniconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3...conda3 by running conda init? [yes|no] [no] >>> yes no change /data/sata_data/workshop/wsu29/mini...1553 days ago
Bash command to install bwa, samtools, picard !
...stall bwa Collecting package metadata (repodata.json): done Solving environm...an ## environment location: /data/sata_data/workshop/wsu29/anac...samtools Collecting package metadata (repodata.json): done Solvin...ll picard Collecting package metadata (repodata.json): done Solvin...1553 days ago
Bash command to install GATK, Bedtools and SnpEff !
...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 | 1.1 MB | ##...1553 days ago
Installing ggplot2 and its dependencies on Ubuntu !
.../bin/cat checking for local ICUDT_DIR... icu61/data checking for gcc... gcc -std...fined and set... no checking for available ICU data library (ucnv, uloc, utrans)....usr/lib/x86_64-linux-gnu -licui18n -licuuc -licudata -L/usr/lib/R/lib -lR install...1548 days ago
- (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ##...
1544 days ago
To convert just one specific read group to fastq
...set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the pro...f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder. mkdir -...1540 days ago
- ...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+dfsg1-2ubuntu1) ... S...
1539 days ago
Install python-numpy python-scipy python-matplotlib on Ubuntu !
...hon-decorator python-matplotlib-data python-olefile python-pil pyt...ython-matplotlib python-matplotlib-data python-numpy python-olefile p...c/universe amd64 python-matplotlib-data all 2.1.1-2ubuntu3 [3,774 kB]...selected package python-matplotlib-data. Preparing to unpack .../09-...1539 days ago
