Results for "C"
Bio-Scripts
Long reads mapper bash script !
...2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scrip to map your long reads and...bin/ngmlr-0.2.3/ngmlr lamsaLoc=/home/urbe/Tools/LAMSA/lamsa...with $toolName" $bwaMemLoc index $refFasta $bwaMemLo...= "ont" ]; then $ngmlrLoc -t $thread -r $refFasta -q $l...2174 days ago
Perl subroutine to read genome/reads fasta file !
...ile = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/){ i...else { $seq=$seq.$_; } } $map{$id} = $seq; close(IN); return \%map; }...2185 days ago
- ...t/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fast...0 -m 25 -s 100000000 --canonical /home/urbe/Tools/trinityrn..._out_dir/read_partitions/Fb_0/CBin_30 Monday, July 9, 2018:...onday, July 9, 2018: 11:18:22 CMD: mkdir -p /home/urbe/Tools/...
2179 days ago
- ...[options] INPUT -A|--accession Replaces accessi...(member): name[,...] -W|--clip Rem...than 1 file, each of which will be suffixed...Current/default is warn -v|...
2178 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, '2177 days ago
- ...\__|\___| ░▓▓▓^▓▓▓░ Transrate v1.0.3 by Richard Smith-Unna, Chris Boursnell, Rob Patro,...Assembly file(s) in FASTA format, comma-separated --left=...teSTAT/Trinity [ INFO] 2018-07-13 14:54:21 : Calculating contig metrics......
2174 days ago
- ...2": "https://osf.io/qfsze/download"} # the sample names are dictionary keys in sample_links. extract them to a list we can use be...# dynamically generate the download link directly from the dictionary download_link...
1567 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting obje...ckages/porechop/misc.py to misc.cpython-36.pyc byte-compilin...(default: 16) Barcode binning settings: Contr...2157 days ago
- set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0...be/Tools/Reapr_1.0.18/reapr facheck WadinetaGapFilled.gapfill...stats $fcdcutoff 03.score echo "[REAPR pipeline] Running b...rbe/Tools/Reapr_1.0.18/reapr fcdrate ./ 01.stats 02.fcdrate...
2150 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; }; chomp...$pals, ($pals+1)*2 ), $p1-$pals; } } __DATA__ AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCG...2150 days ago
