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" %in...2294 days ago
2274 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2273 days ago
Perl script to convert fastq to fasta file
...$factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object $seqret->run({-sequence => $infile, -sformat1 => 'fastq', -o...2261 days ago
Plot custom gene density with R
library(karyoploteR) pp2260 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/...rial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome...treads to be used in the run. eg: 1,2,3,..etc. #-C -both-stra...ere "?" = 30 jellyfish histo -o 19mer_out.histo 19mer_out #P...2256 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2164 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2249 days ago
Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2249 days ago
Perl script to count the number of files in a directory with regex
...t; use warnings; my @allNames=("_D14_","_B14_","_B15_","_C1T1_","_C3T3_",...12_","_D13_","_E1B1_","_E1B3_","_H001_","_H3-03_","_H3-04_","_HB0_"...33_","_B3B1_","_C210_","_C211_","_C21_","_C24_","_C27_","_E2B2_","_...24_","_A3B1_","_C2B4_","_B22_","_H3-14_","_Hprim54_","_Hprim12_","_...2247 days ago