Extract all fasta sequences except ids !
awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' genomic.fna > filtered_without_omi.fasta #extract subseq seqtk subseq omi_ids....asta > omi_single_id_plus_all.fa #Extract unique kmer ./uniquekmer -f..._kmer19_formated.fa fastawrap=19 #Extrac...820 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input: cat > in.fasta BGI...: grep -f gene_ids.txt ids_gene_ids.tsv | cut -f1 > ids.selected.txt # Extrac...816 days ago
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to perform operations on general feature format (GFF) and general...on compatible with the linux we’re using so we will just download, extract, and make a symlink. # download and extrac...816 days ago
816 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RN...install we can just download this distribution and extract it. Like with our other progr...mlink to make it easier to find. # download and extrac...816 days ago
Extract the mapped and unmapped reads !
PROCESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam...582 days ago
87 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file...e.gff'; my $genome_fasta = 'path/to/your/genome.fasta'; # Gene ID to extract my $gene_id_to_extrac...87 days ago