Results for "query"
Bio-Scripts
Download genome using NCBI esearch command line !
...g command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format...1115 days ago
R script to visualize fastANI core-genome comparison
...parison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] s...1115 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...est::Common; my %param = ( query => undef, outputFil...('bundling'); GetOptions( 'q|query=s' => \$param{query},...); } if ( !( defined( $param{query} ) ) or !( defined( $par...could not be parsed. Resubmitting query.\n" ); sleep(10);...2929 days ago
Blast result parser with Perl and Bioperl
...er, length, description, E value, bit score, query frame, query start, query end, hit start,...info for tab-deliminated columns print OUT "query_name\tquery_length\taccession...# get the frame of the query sequence print OUT $hsp-...2928 days ago
Blast script to index and extract sequence !!
...ATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGCTTCTGAACTG GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC .... # query the blast database by id and...2865 days ago
BASH script for SelfBLAST a genome
...SEQ=$FASTAFILE else echo "Something went wrong $USER - Contact jitendra" fi echo "Doing alignments -- BLASting"; blastn -task megablast -query $SEQ -db $MYDB -evalue 1e-5 -...2665 days ago
Create genome scaffolding with Perl
...ome =head1 SYNOPSIS ./psl_scaffolder.pl -query [options] =cut sub mi...my @pslFiles = (); my $projOpts = { "query" => 0, # contig file for quer...} } @ARGV = @pslFiles; if(!$projOpts->{"query"}){ pod2usage({-exitVal =>...2322 days ago
Perl script to run SATSUMA in loop !
...; # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "rename...2154 days ago
Installing pb-assembly on Linux !
...aph_to_contig fc_primary_contig_index.pl fc_select_reads_from_bam.py fc_contig_annotate fc_graph_to_utgs fc-query fc_unzip...2048 days ago
To convert just one specific read group to fastq
...data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get the project run information. esearch -db sra -query $PROJECT | efetch -format ru...1556 days ago
