2061 days ago
2047 days ago
Setting up falconUnzip conda environments for genome assembly !
...conda3/envs/denovo_asm added / updated specs: - pb-assemb...83 KB conda-forge setuptools-40.6.2 |...c_1 bioconda setuptools: 40.6.2-py2...sure that releases on Bioconda live up to the # # quality that Pac...2033 days ago
Resume the MIRA assembler run !
...fest_file ...] Options: -c / --cwd= directory Change working directory -r / --resume Resume an interupted assembly -h / --help...1777 days ago
Samtools commands for bioinformatician !
...l_sej_sorted.bam ### indexing sorted file # ouput is file.bai # always index...bam.bam ### identifying genome variants (mpileup command) # -g : output is bc...-a : at all positions samtools depth -a sorted_dupremoved.bam > depth.txt ###...1646 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) { #print "current line: $_ -- next line: $next_line$/...1603 days ago
Bash script to alignment of short reads against reference genome !
...sambamba sort SRR1770413.raw.bam sambamba markdup SRR1770413.raw.sorted.bam SRR...ny threads" and also "give the reads the read group K12 and the sample name K12"...file, writing it to .sorted.bam. #marking PCR duplicates: sambamba markdup SRR1...1602 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
#Inspired from online search sudo apt-get update sudo apt-get install gcc sudo apt-get install make sudo apt-get install libbz2-dev sudo apt-get install zlib1g-dev sudo apt-ge...1601 days ago
Bash commandline to install Anaconda !
...Current Dload Upload Total Spent Left...: lxml-4.3.2-py37hefd8a0e_0 ... installing: markupsafe-1.1.1-py37h7b6447c_0 ......sortedcontainers-2.1.0-py37_0 ... installing: soupsieve-1.8-py37_0 ... installi...1598 days ago
Bash command to install Miniconda !
...sata_data/workshop/wsu29/miniconda3 added / updated specs: - _libgcc_mu...- ruamel_yaml==0.15.46=py37h14c3975_0 - setuptools==41.4.0=py37_0 - si...nux-64::ruamel_yaml-0.15.46-py37h14c3975_0 setuptools pkgs/main/linux-...1598 days ago