Results for "single-molecule physical genome mapping"
Bio-Scripts
# 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 dataframe192265 days ago
Plot custom gene density with R
library(karyoploteR) pp2250 days ago
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.fastq #-t -treads=unit32 Number of tread...2246 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
2210 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X...' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome | awk '{ FS = "\t" } ; BEGIN{L...
2210 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner +...indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python...2124 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 genome....2141 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis...reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome...2141 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::D...ly including the promoter) ### First, index the genome my $file_fasta = $ARGV[0];...y $db = Bio::DB::Fasta->new($file_fasta); print ("Genome...2139 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...
2138 days ago
