Results for "Unique molecular identifiers"
Bio-Scripts
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO...display_id; my $seq = $seqs->seq; unless(exists($unique{$seq})) { $outseq->write_seq($seqs); $unique{$seq...2688 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/dow...dividual. EstimateLibraryComplexity (Picard) Estimates the numbers of unique mole...
2073 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for jit: R version 3.4.4...ng -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o g...1548 days ago
- #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompres...ght tool for processing biological data (FASTA/FASTQ). if you have a list of identifiers that you would like to extrac...
1400 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa ou...rue Writing chunk 1 Waiting for writing to finish. Finished. snpRate=0.0, max=0, unique=true...988 days ago
Extract all fasta sequences except ids !
awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' genomic.fna > filtered_without_omi.fasta #extract su..._id.fa filtered_without_omi.fasta > omi_single_id_plus_all.fa #Extract unique kmer ./uniquekmer...826 days ago
- #!/bin/bash #Counting k-mers for different k echo "k,unique,distinct,total" for k in {1..15}; do kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1 egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\ END{print "'$k',"u","d","t}' done
792 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length = 2, $max-repeat-length = 6, $min-repea...es.push($substring); } } } return @microsatellites.unique; }...92 days ago
