Results for "Gene expression"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.or...en(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-regio...1126 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matches the regex print it if it matches while($line = ){...2907 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "canno...ANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene lengt...2907 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::Esca...2906 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id = 0; open F,"$ARGV[0]...@val = split /\s+/, $_; my @newval=@val; shift @newval; print ">$id [ gene=$val[...
2503 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, lo...rary(ggplot2) } # import a text file with gene positions # columns should b...chr, position (no end or gene name required) genes...2275 days ago
Plot custom gene density with R
library(karyoploteR) pp2240 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number...# extract the two values or columns with a regular expression # A group of letters and a...sequence in segments of length # three, a regular expression will be used searching for al...2145 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Seq...>$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outfile_upstre...the stop codon) # gene - the entire gene seque...2129 days ago
- ...lsToFastq (Picard) Generate FASTQ file(s) from Illumi...het sites for allele specific expression CollectAllelicCoun...Picard) Generate index statistics from a B...r Generates recalibration table for Base Q...
2066 days ago
