Results for "fasta"
Bio-Scripts
...401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...938 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa938 days ago
Bash script to simulate a genome !
...45.1_ASM340174v1_genomic.fna_upper.fasta.gz # Convert to dipl...45.1_ASM340174v1_genomic.fna_upper.fasta.gz \ ow=t \ vcf=GCA_0034017...340174v1_genomic.fna_upper.diploid.fasta.gz|\ /genetics/elbers/bin/se...340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...927 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas899 days ago
Run Pango on your multifasta file !
....html (base) [jnarayan@hn1 FASTA]$ conda activate pangolin (pangolin) [jnarayan@hn1 FASTA]$ ls Input_for_Cova_all_samp...a (pangolin) [jnarayan@hn1 FASTA]$ pangolin --update pangolin...en to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv (pangolin...897 days ago
Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/minikraken_...w5 -A1 -B2 -O3,13 -E2,1 -s200 -z200 -N50 --min-occ-floor=100 finaal_output.fasta finaal_output.fasta > finaal_...886 days ago
- bowtie2-build toy_dataset_contig_for_mapping.fasta toy_dataset_contig_for_mapping.btindex bowtie2 -x toy..._dataset_contig_for_mapping.btindex -f -U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species...
877 days ago
Perl script to rename the fasta file !
#Script #1 #!/usr/bin/perl -w use strict; #USAGE #perl extractPattern.pl kmerfasta > uniref100_result_broad my %kHash; local $/ = '>'; my $infile2 = "$ARGV[0]"; # Kmer fasta open( FH2, '868 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.fasta861 days ago
Extract all fasta sequences except ids !
...f=!l[$1]}f' genomic.fna > filtered_without_omi.fasta #extract subseq seqtk sub...est cat omi_single_id.fa filtered_without_omi.fasta > omi_single_id_plus_all.fa...t the kmer of omi seqtk subseq kmercollection.fasta ../omi_single_id.txt > omi_km...838 days ago
