Results for "Data Mining Algorithm"
Bio-Scripts
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted....i > aln-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=data/Cdif...2044 days ago
- $ sudo apt install npm Reading package lists... Done Building...e-nopt node-normalize-package-data node-npmlog node-once node...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]...ackage node-normalize-package-data. Pr...
1593 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $ne...$next_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ a...1600 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. fastq-du...in the SRA toolkit. It allows directly downloading data f...fastq-dump --split-files SRR1770413 #SRA stores data in a...1599 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 SRR...he only major change from bwa mem is that we'll tell it we're working with short read data usin...1599 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ c...now be installed into this location: /data/sata_data/workshop/wsu29/anaconda3...1-py37_0 ... installing: importlib_metadata-0....2-py37_0 ... installing: pytest-remotedata-0.3....1595 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest...Miniconda3 will now be installed into this location: /data/sata_data/w...ing conda init? [yes|no] [no] >>> yes no change /data/sata...1595 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environment:...lan ## environment location: /data/sata_data/workshop/wsu29/anac...l samtools Collecting package metadata (...all picard Collecting package metadata (rep...1595 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...# environment location: /data/sata_data/workshop/wsu29/anac...a727_0 193 KB r-gdata-2.18.0 | r36h6...################# | 100% r-gdata-2.18...1595 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] pa...at checking for local ICUDT_DIR... icu61/data checking for gcc... gcc -std...and set... no checking for available ICU data l...b/x86_64-linux-gnu -licui18n -licuuc -licudata -L/u...1590 days ago
