Results for "New Genome"
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...2248 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
2212 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtoo...IN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome | awk '{ FS = "\t" } ; BEGIN{...
2212 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script...e distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Depend...2142 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage per...e reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinet...2142 days ago
Perl script to convert GFF 2 FASTA !
...my $outfile_pep = Bio::SeqIO->new( -format => 'fasta', -file =>...y $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file =>...oter) ### First, index the genome my $file_fasta = $ARGV[0]; my $db = Bio::DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ###...2141 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/u...canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metazoa_odb9 -o GRAALHaploid_BUSCO -m genome -f #Plot BUSCO python B...
2139 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($_ =~ /^>...2135 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage:...al-filter Filter used in early 1000 Genomes data: no...lter-1 Filter used in current 1000 Genomes data Filters based on al...
2128 days ago
- ...Collect whole genome sequencing-related metrics...rage and performance of whole genome sequencing (WGS) experimen...e reads in a file to a single new read-group. ApplyBQSR...rom a reference sequence to a new FASTA file. FindBadGenomicK...
2077 days ago
