Results for "Count"
Bio-Scripts
Clump Finding Problem Solved with Perl
...kmerMatch ($string, $subStr, $kmer); sub kmerMatch { #Check the exact matching kmers with sliding window my ($string, $myStr, $kmer)=@_; my $count=0; for (my $aa=0; $aa...2338 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
2268 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_e...treads to be used in the run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m -mer-len...2250 days ago
Perl script to count the number of files in a directory with regex
#!/usr/bin/perl use strict; use warnings; my @allNames=("_D14_","_B14_","_B15_","_C1T1_","_C3T3_","_D12_","_D13_","_E1B1_","_E1B3_","_H001_","_H3-03_","_H3-04_","_H...2241 days ago
Perl script to count number of Ns in a multifasta file !
...Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa Result ➜ SSPACED_P2 perl countN.pl out.fasta scaffold1_size...2148 days ago
- ...---------------------------- CMD: jellyfish count -t 40 -m 25 -s 100000000 --c...-t 40 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (6 seconds)...------------------ * Running CMD: jellyfish count -t 40 -m 25 -s 100000000 --c...
2131 days ago
Install Parrot Virtual Machine !
...oc - Is perldoc installed.................................no. auto::coverage - Are coverage analysis tools installed...Negative repeat count does nothing at lib/Parrot/Co...1541 days ago
- ...chosen columns from each file. CreateReadCountPanelOfNormals...BETA Tool) Creates a panel of normals for read-count denoising DenoiseReadCou...(Picard) Identifies duplicate reads, accounting for mate CIGAR. Mer...
2079 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent....2057 days ago
- ...prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o count.o count.c cc -std=c99 -O3 -Wall -Wmi...
2030 days ago
