Results for "multiple fasta"
Bio-Scripts
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$text" | sed 's/ //g' OR echo "$text" | awk '{ gsub(/ /,"");...GAGGGRTTT echo "$text" | sed 's/^ //g' echo "$text" | sed 's/ \$//g' #Multi...1000 days ago
- ...ry File [File In] default = stdin -A Multiple Hits window size (zero for si...zero) [Real] default = 7.0 -P 0 for multiple hits 1-pass, 1 for single hit...Optional -U Use lower case filtering of FASTA sequence [T/F] Optional...
994 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced...et ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz bin/pfilt uniref90.fasta...994 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options]...cid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT Nucle...tide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB Amino...986 days ago
- # make reference for randomreads.sh # randomr...ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...
972 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa972 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp1...ASM340174v1_genomic.fna_upper.fasta.gz # Convert to dipl...ASM340174v1_genomic.fna_upper.fasta.gz \ ow=t \ vcf=GCA_0034017...4v1_genomic.fna_upper.diploid.fasta.gz|\ /genetics/elbers/bin/se...4v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslas...962 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas933 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/reso....html (base) [jnarayan@hn1 FASTA]$ conda activate pangolin (pangolin) [jnarayan@hn1 FASTA]$ ls Input_for_Cova_all_samp...a (pangolin) [jnarayan@hn1 FASTA]$ pangolin Input_for_Cova_all...en to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv (pangolin...931 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_...921 days ago
