Results for "Image data analysis"
Bio-Scripts
(denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'gi...-sym.makefile 'greg200k-sv2.2' curl -L https://downloads.pacbcloud.com/public/data/git...2049 days ago
- #! /usr/bin/Rscript ## Collect arguments args
2018 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@S...-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=data/Cdi...2018 days ago
Setting up falconUnzip conda environments for genome assembly !
...$ 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...2004 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...
1568 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) {...line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__...1575 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...1574 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...1574 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tm...stalled into this location: /data/sata_data/workshop/wsu29/anaconda3...a-2.8-py37_0 ... installing: imagesize-1.1.0-py37_0 ... instal...... installing: pytest-remotedata-0.3.1-py37_0 ... installing:...1570 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...1570 days ago
