Results for "1"
Bio-Scripts
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -format => 'fasta'...2149 days ago
Long reads mapper bash script !
...lamsaLoc=/home/urbe/Tools/LAMSA/lamsa #Parameters accepted toolName=$1 refFasta=$2 longReads=$3 t...echo "#USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont" exit 1 fi fileName=$(basename "$...2133 days ago
- ...ort/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fas...unning CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kme..._0/CBin_31 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /hom...dir/read_partitions/Fb_0/CBin_166 Monday, July 9, 2018: 11:1...
2138 days ago
- ...Filter used in early 1000 Genomes data: no...sequences starting or ending with >= 10N --qual-filter-1...than 1 file, each of which will be s...ots' for tool ./fastq-dump : 2.9.1 ( 2.9.1-1 )
2137 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2136 days ago
- ...\___| ░▓▓▓^▓▓▓░ Transrate v1.0.3 by Richard Smith-Unna, C...ng three kinds of metrics: 1. sequence based (if --assembl...ly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate --...88 [ INFO] 2018-07-13 14:54:34 : n with orf...
2133 days ago
- ..."ERR458500":"https://osf.io/xju4a/download", "ERR458501": "https://osf.io/nmqe6/downl...ample_links.keys() # download yeast rna-seq data from Schurch et al, 2016 study rule download_all:...
1526 days ago
Installing Porechop on Ubuntu !
..... remote: Counting objects: 1579, done. remote: Total 1579 (delta 0), reused 0 (delta...echop: make -j 8 g++ -std=c++14 -Iporechop/include -fPIC -O3...ogress information: 0 = none, 1 = some, 2...(0 to 100) (default: 90.0) --check...2116 days ago
- ...echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0.18/reapr WadinetaGapFilled....aGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipel...core" /home/urbe/Tools/Reapr_1.0.18/reapr score -P 5 00.ass...tats" /home/urbe/Tools/Reapr_1.0.18/reapr stats -p /home/ur...
2109 days ago
Perl script to find palindromic pattern !
...T G C A ]; my $in = do{ local $/; }; chomp $in; print $in; for my $p1 ( 1 .. length( $in ) -2 ) {...0; for my $p2 ( 1 .. $p1 -1 ) { last unless substr( $in, $p1-$p2, 1 ) eq $invert{ substr $...2109 days ago
