Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/minikraken_20171019_8GB.tgz out.fa more out.fa_class.txt | grep "227859" | awk '...873 days ago
Extract the sequences with IDs !
#sed -i 's/\_/ /g' Delta_seqID_from_lineage_report.txt seqtk subseq genomic.fna Delta_seqID_from_lineage_report.txt > Delta.fasta #Split the fasta in 11 equal sequences subsets pyfasta split -n 11 Delta.fasta848 days ago
Extract all fasta sequences except ids !
...genomic.fna > filtered_without_omi.fasta #extract subseq seqtk subseq omi_ids....out_omi.fasta > omi_single_id_plus_all.fa #Extract unique kmer ./uniquekmer -f...a out=omi_kmer19_formated.fa fastawrap=19 #Extract and number the kmers perl st...825 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:...rep -f gene_ids.txt ids_gene_ids.tsv | cut -f1 > ids.selected.txt # Extract fasta sequence that correspon...820 days ago
Install Install Gffcompare on Ubuntu / Linux
...transfer format (GTF) files. It has a binary distribution compatible with the linux we’re using so we will just download, extract, and make a symlink. # download and extract cd ~/workspace/bin wget htt...820 days ago
820 days ago
Install StringTie on ubuntu / Linux !
...are available so to install we can just download this distribution and extract it. Like with our other progr...ms we also make a symlink to make it easier to find. # download and extract cd ~/workspace/bin wget htt...820 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...587 days ago
91 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
...file and genome FASTA file my $gff_file = 'path/to/your/file.gff'; my $genome_fasta = 'path/to/your/genome.fasta'; # Gene ID to extract my $gene_id_to_extract = 'your_gene_id'; # Step 1...91 days ago