Results for "Genome Size"
Bio-Scripts
Create genome scaffolding with Perl
...psl_scaffolder.pl - use self-mapped PSL file to scaffold a genome =head1 SYNOPSIS ./psl_s...rbose => 0}); } ## calculate percent identity my $qAliSize = $qEnd - $qStart; my $tAliSize = $tEnd - $tStart; my $siz...2310 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, load it, # if not, install and load it if("ggplot2" %...2286 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2266 days ago
Plot custom gene density with R
library(karyoploteR) pp2251 days ago
Estimate Genome Size with Jellyfish and R
...5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read_2.fast...er-len=unit32 Length of the k-mer #-s -size=unit32 Hash size / memory allocation #-o...2248 days ago
- zero=$(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 samtools mpileup mapping_result_sorted....IN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgeno...
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 to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl geno...2142 days ago
Perl script to run SATSUMA in loop !
...sta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinet...UMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids;...2142 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB...ely including the promoter) ### First, index the genome my $file_fasta = $ARGV[0];...my $db = Bio::DB::Fasta->new($file_fasta); print ("Geno...2141 days ago
