Results for "PA"
Bio-Scripts
Perl script to count number of Ns in a multifasta file !
...nvert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa Result ➜ SSPACED_P2 perl countN.pl out.fast...2196 days ago
Perl script to run SATSUMA in loop !
...MA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the ids if ($ARGV[1] eq "ids") { my $idFile="palindrome_ids.txt"; open my $h...2192 days ago
Perl script to convert GFF 2 FASTA !
...omoter) ### First, index the genome my $file_fasta = $ARGV[0]; my $db = Bio::DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ### Second, parse the GFF3 my %CDS; my %CD...2191 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/augustus-3...
2189 days ago
Long reads mapper bash script !
...ngmlr lamsaLoc=/home/urbe/Tools/LAMSA/lamsa #Parameters accepted toolName=$1...eads > $fileName.out.sam elif [ $readsType == "pacbio" ]; then $lamsaLoc...echo "MINIMAP2:Please specify reads type: ont, pacbio" fi elif [ $toolName =...2175 days ago
- ...mer occurrences... done parsing 59324464 Kmers, 59324464...1 --DS --num_threads 6 --PARALLEL_IWORM > /home/urbe/Too...y-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_36 Monday,...y-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_175 Monday...
2179 days ago
- ...r by value: pass|reject|criteria|redacted...coordinates --matepair-distance Filter by distan...r by value: pass|reject|criteria|redacted...
2178 days ago
- ...rd Smith-Unna, Chris Boursnell, Rob Patro, Julian Hibberd, and S...ly file(s) in FASTA format, comma-separated --left=...3 : Loading assembly: /media/urbe/MyPassport/BorisTrinityAssembly/Tr...No reference provided, skipping comparative diagnostics [ INFO] 20...
2175 days ago
- ...from Schurch et al, 2016 study rule download_all: input: expand("rnaseq/raw_data/{sample}.f...rule download_reads: output: "rnaseq/raw_data/{sample}.fq.gz" params: # dynamically g...
1568 days ago
Installing Porechop on Ubuntu !
.../anaconda3/lib/python3.6/site-packages/porechop copying build.../anaconda3/lib/python3.6/site-packages/porechop copying build.../anaconda3/lib/python3.6/site-packages/porechop-0.2.3-py3.6.eg...D_SIZE The number of base pairs at each end of the read...2158 days ago
