Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2083 days ago
Perl script to create a consensus of nucleotide sequences !
use strict; use warnings; my @instances = qw ( AAAAA ATCGA ATAAA ); my @instances2 = qw ( AAAAA AACGA ATAAA AGAAA AGAAA); print consensus(@instances),"\n";...2059 days ago
Installing pb-assembly on Linux !
...arayan@hmem00 ~]$ conda config --add channels bioconda [jnarayan@hmem00 ~]$ conda config --add channels conda-forge [jnarayan@hmem00 ~]$ conda create -n denovo_asm [jnarayan@hm...2062 days ago
Installing Platypus on Ubuntu !
.../man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig mkdir: cannot create directory ‘/usr/local/include/htslib’: Permission denied mkdir: cannot create directory ‘/usr/local/share/m...2047 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Proceed ([y]/n)?...2017 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "1999 days ago
1828 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % R...1583 days ago
Install snakemake and activate on conda
$ conda create -c bioconda -c conda-forge -n snakemake snakemake $ conda activate snakemake1566 days ago
To convert just one specific read group to fastq
...e reads folder. mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mk...1570 days ago