Results for "PA"
Bio-Scripts
...CRATE"], ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], ); for my $word_pair (@tests) { #Nice way to split the values my ($w1, $w2) = @$word_pair; my $simw = simw $w1,...1852 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download Ubuntu / Debian sudo a...-blast-2.8.1+-x64-linux.tar.gz # add BLAST location to system PATH export PATH=$HOME/tools/BL...
1814 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands...s 3318 cat ch101_read33155_template_pass_FAH31515.faa mutant3CH101.f...5CH101.fasta mutant153CH101.fasta > allPalindromeSimulated.fa 3319 ~...ed.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk...1788 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1777 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
1775 days ago
Perl script to run in parellel !
...use strict; use warnings; use Parallel::ForkManager; use Bio:...SeqIO; my ($sequence_data_ref) = parse_genome_files($ARGV[0]); m...; my $n_processes = 4; my $pm = Parallel::ForkManager->new( $n_p...print "starting XFOIL instance with parameters $chr_set!\n"; to...1739 days ago
Samtools commands for bioinformatician !
...ands ### calling snp and indels with no frequency threshold # omit -v parameter bcftools call -c sal_...d.bam.bam sal_ref_sej.fasta ### results into txt file samtools depth /path/to/sorted_bam.bam > /path/t...1655 days ago
Bash script to download SRA file !
...directly pull the sequence data (in paired FASTQ format) from the ar...ws directly downloading data from a particular sequencing run ID...SRR1770413 #SRA stores data in a particular compressed format (SR...r the first and second mate in each pair. We'll use them in this for...1611 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
...https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 tar -vxjf bcftools-1.9.tar.bz2 cd bcftools-1.9 make export PATH="$PATH:/usr/bin/bcftools-1.9" exp...1610 days ago
Bash commandline to install Anaconda !
...1.0.6-h14c3975_5 ... installing: expat-2.2.6-he6710b0_0 ... instal...-1.1.1b-h7b6447c_1 ... installing: patchelf-0.9-he6710b0_3 ... ins...th-1.1.0-py37_0 ... installing: msgpack-python-0.6.1-py37hfd86e86_1...nose-1.3.7-py37_2 ... installing: pango-1.42.4-h049681c_0 ... ins...1607 days ago
