Results for "Mate pair sequencing"
Bio-Scripts
#!/usr/local/bin/perl -w # NOTE: YOU MUST CHANGE THE LINE ABOVE TO POINT TO # THE FULL PATH OF THE PERL EXECUTA...parameters,databases are are roughly 150k per base-pair of se...2692 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...] ./fastq-dump...re 1-based coordinates --matepair-distance Filter by distance between matepairs....
2126 days ago
- ...Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g....e of several filters. FixMateInformation (Picard)...ed by the engine AnnotatePairOrientation (BE...
2075 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta...the contig id to the NNNNN regions found. #Each region is represented as a pair "$ini...2062 days ago
- #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupa...sStar.c nsStar.c: In function ‘nsStarPairsOrParensFull’: nsStar.c:30:1...../../../src/shared/constants -c -o pairsPr.o pairsPr.c pairsPr.c: In..../../shared -I../../../src/shared/rng pairs.o -o...
2026 days ago
- ➜ Tools git:(master) ✗ wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 --2018-...est/xx#large_aux_java.cram htslib-1.9/test/xx#minimal.sam htslib-1.9/test/xx#pair.sam...
2019 days ago
Bash script to download SRA file !
...lkit to directly pull the sequence data (in paired FASTQ format) from the arch...directly downloading data from a particular sequencing run ID fastq-dump --...get two files, one for the first and second mate in each pair. We'll use them in this format when...1559 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.fa...nd the input alignment files. The first file should contain the first mate, the second file the second mate. #co...1559 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257...cess is to extract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1...1542 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-...ly. BiostatisticsBiostats materials ... Biostatistics is an...Rahul Nayak@rahul GeneMates: an R package for Detecting Horizo...n bacteria using whole-genome sequencing (WGS) data. It is particularl...1511 days ago
