Command line to create blast uniref database !
...gp' program is available in the legacy NCBI BLAST package (no longer supported), which is available from the NCBI's FTP site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2....960 days ago
Command line to download blast database / protein
...NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database deta...eq #First run this to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #ca...953 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x...952 days ago
952 days ago
Downloading mmseqs databases !
....org - NR Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB...952 days ago
Installing Covid19 Environment !
...############################################################# | 100% libgomp-11.2.0 | 427 KB |...############################################################# | 100% pango-1.48.10 | 400 KB |...934 days ago
Bash script to simulate a genome !
.../elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/...Convert to diploid with approximately 2% heterozygosity rate, max indels=20bp #...grep -v ">"|wc -m # 140687135 # 2% heterozygosity is how many bases calc 0...928 days ago
912 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} $1 in tgts' enriched_ids_list result/GO.out > enriched_GO.out.xls905 days ago
Run Pango on your multifasta file !
..._all_samples_combined.fa (pangolin) [jnarayan@hn1 FASTA]$ pan...FASTA]$ pangolin --update pangolin already latest release (v3...me/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-package...1 1 pangolearn 1...897 days ago