Results for "5"
Bio-Scripts
...age script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {...erage > chr1_MA605.coverage #awk '$1 == 2 {print $0}' deduped_MA605.coverage > chr2_MA605.coverag...2062 days ago
Setting up falconUnzip conda environments for genome assembly !
...--------------- python-2.7.15 | h33da82c_5 13.6 MB conda-forge...| py27_1001 150 KB conda-forge pycpars...mummer4-4.0.0beta2 | pl526hfc679d8_3 1.3 MB b...numpy: 1.15.0-py27h1b885b7_0...2048 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, "2030 days ago
Backward Elimination with Python
...e(x, j, 1) regressor_OLS.summary() return x SL = 0.05 X_opt = X[:, [0, 1, 2, 3, 4, 5]] X_Modeled = backwardElimin...continue regressor_OLS.summary() return x SL = 0.05 X_opt = X[:, [0, 1, 2, 3, 4,...2013 days ago
Palindrome Simulation commands !
...ssemblySim more allCommands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101...id=97 3316 mutate.sh in=mutant15CH101.fasta out=mutant153CH101...515.faa mutant3CH101.fasta mutant15CH101.fasta mutant153CH101.fas...allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paire...1794 days ago
- #!/bin/bash cd `pwd` perl ~/apps/SSPACE-1.2_linux-x86_64/SSPACE_v1-2.pl \ -l libraries.txt \ -s Contigs_over200_nocp.fasta \ -k 5 \ -a 0.7 \ -x 1 \ -m 30 \ -o 20 \ -b Rayk31_scaffolds_extension
1781 days ago
Perl script to run in parellel !
...n" or die $!; system ("augustus --species=caenorhabditis --outfile=$fn $seq --AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/Alienomics_v1.1/augustus.2.5.5/config"); close FILE or...1744 days ago
- ...#" | awk -F "\t" '{if (!match($NF, "0/1")) print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$8}' | tr ';' ' ' | sed s/...'{if ($6 >= WEIGHT) print $0}' | awk -v SUM=0 '{if (length($4) == length($5)) { SUM+=length($4); } else i...
1662 days ago
Bash script to alignment of short reads against reference genome !
...0 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1...name K12" #reference and FASTQs E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR...G\tID:O104_H4\tSM:O104_H4' \ E.coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR...1617 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
...gcc sudo apt-get install make sudo apt-get install libbz2-dev sudo apt-get install zlib1g-dev sudo apt-get install libncurses5-dev sudo apt-get install libncursesw5-dev sudo apt-get install lib...1616 days ago
