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";...2064 days ago
1757 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converting sam...1635 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 \ | samtools view -b - >SRR1770413.raw.bam sambamba sor...1591 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for jit: R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The...1582 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ sudo apt install libpar-packer-perl Reading package lists... Done...1543 days ago
Create random 10000 SNPs in genome !
...files .. Generating the correspondance map for genomic variants introduced during simulation: simuSNP.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants...1243 days ago
Create random 1000 INDEL in genome !
...les .. Generating the correspondance map for genomic variants introduced during simulation: simuINDEL.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants...1243 days ago
Create random 1000 CNVs in genome !
...files .. Generating the correspondance map for genomic variants introduced during simulation: simuCNV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants...1243 days ago
Create random 5 inversions in genome !
...files .. Generating the correspondance map for genomic variants introduced during simulation: simuINV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants...1243 days ago