Results for "C"
Bio-Scripts
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.fas950 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base) [jnarayan@hn1 FASTA]$ conda activate pangolin (pango...les_combined.fa All dependencies satisfied. The query file...1 align_to_reference 1 1...948 days ago
Omicron Sequences accession number !
EPI_ISL_6647956 EPI_ISL_6647957 EPI_ISL_6647958 EPI_ISL_6647959 EPI_ISL_6647960 EPI_ISL_6647962 EPI_ISL_6647961 Search the IDs in https://www.epicov.org/epi3/frontend945 days ago
Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/mi...ikraken_20171019_8GB.tgz out.fa more out.fa_class.txt | grep "227859" | awk...5 -A1 -B2 -O3,13 -E2,1 -s200 -z200 -N50 --min-occ-floor=100 finaal_output.fast...937 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_species1.sam samtools sort toy_...
928 days ago
- ...vo-ideapad-320-15ISK:~/VANSH$ conda update -n base conda Collecting package metadata (current_repodata.json): done S...15.3 MB The following packages will be UPDATED: ba...################## | 100% backports.functools_ | 9 KB...
923 days ago
- #To update the linux OS -- run the following sudo -- sh -c 'apt-get update; apt-get upgrade -y; apt-get dist-upgrade -y; apt-get autoremove -y; apt-get autoclean -y' #OR sudo apt-get update && sudo apt-get upgrade
920 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, '918 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.fasta911 days ago
- You have to compile the code with a C++ compiler. TDM-GCC MinGW compiler which you can download from this link: https://sour...c/ Once you download and install the compiler, you need to open the...e commands: g++ -o NewFileName TrojanCockroach.cpp g++ -o NewFileNa...
910 days ago
