Results for "Bonobo and Neandertal genome sequencing"
Bio-Scripts
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read_2.fast...he run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m...2252 days ago
- zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc
2216 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted...N_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome | a...
2216 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| =...distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa...filename = shift @_; my $filehandle; if ($filename =~ /gz$/)...} else { open $filehandle, "$f...2146 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile);...file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinet...s") { my $idFile="palindrome_ids.txt"; open my $handle, '2146 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use B...ted sequence (starting with ATG and ending...e gene sequence (including UTRs and introns) # upstream3000 - the 3...omoter) ### First, index the genome my $file_fasta = $ARGV[0];...sta->new($file_fasta); print ("Genome fas...2145 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin ex...anuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metazoa_odb9 -o GRAALHaploid_BUSCO -m genome -f...
2143 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/)...2139 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-...filename(s) and deflines (only for single...Filter used in current 1000 Genomes data Filters based on al..."chr1" or "1"). "from" and "to" are 1-based...are placed in files *_1.fastq and...
2132 days ago
- ...ES/FILE gatk forwards commands to GATK and adds some sugar for submittin...Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g....Collect whole genome sequencing-related metrics. Colle...
2081 days ago
