Results for "Store"
Bio-Scripts
Download the genome from NCBI using bash script/command
..." filename="${filename%.*}" # Create a directory with appending G mkdir "G$filename" cd "G$filename" # take action on each file. $f store current file name wget --i...2526 days ago
Download the gff files from NCBI using bash script/command
...filename="${filename%.*}" # Create a directory with appending G mkdir "GFF$filename" cd "GFF$filename" # take action on each file. $f store current file name head -n...2517 days ago
Loop over with all files in a directory in bash
...LES do if [ ${f: -4} == ".fna" ]; then echo "Processing $f file..." ff=$(basename "${f%.*}") echo $ff # take action on each file. $f store current file name mkdir $f...2325 days ago
Perl script to find coding regions in DNA sequences
...calar(@seql)) { chomp($seql[$i]); $seq = $seq . $seql[$i]; $i = $i + 1; } $seq = "\U$seq"; # we are going to use the array @codons to store all of the codons in # the i...2149 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 clustalRead...2134 days ago
Perl script to run SATSUMA in loop !
...ols/SATSUMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the ids if ($ARGV[1] eq "ids...2134 days ago
To convert just one specific read group to fastq
...info.txt # Select the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder....1536 days ago
Tadpole is 250x faster than SPADes assembler !
...minprob for the primary kmer counts. threads=X Spawn X hashing threads (default is number of logical processors). rcomp=t Store and count each kmer together...970 days ago
Split the string with underscore and store values in array with AWK !
more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}' #Other extraction more enriched_ids | grep "WP_" | awk '{split($2,a,"_"); print a[4]"_"a[5]}'> enriched_ids_list awk 'NR==FNR{tgts[$1]; next} $1 in tgts' enriched_ids_list result/GO.out > enriched_GO.out.xls888 days ago
