Results for "R"
Bio-Scripts
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/f...urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/gra...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.ou...= "pacbio" ]; then $ngmlrLoc -t $thread -r $refFasta -q...2131 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while...$_; } } $map{$id} = $seq; close(IN); return \%map; }2142 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPa...26 CMD: cat /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/tri...ome/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/r...-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_135...
2136 days ago
- ...NPUT -A|--accession Replaces accession derived from in...g with >= 10N --qual-filter-1 Filter use...according to splitting criteria....eading disable multithreading -h|--help...
2135 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, '2134 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate _...CRIPTION: Analyse a de-novo transcriptome assembly using thr...comma-separated --reference=...saved in /media/urbe/MyPassport/BorisTrinityAssembly/transra...
2131 days ago
- ...list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5dau...ownload", "ERR458500":"https://osf.io/xju4a...nary keys in sample_links. extract them to a list we can use...download_link = lambda wildcards: sample_links[wildcards.sam...
1524 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting ob...ges/porechop/porechop.py to porechop.cpython-36.pyc byte-com...-v VERBOSITY, --verbosity VERBOSITY...2114 days ago
- set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0.18/reapr WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out...bam 01.stats $fcdcutoff 03.score echo "[REAPR pipeline] Ru..."[REAPR pipeline] Running fcdrate" /home/urbe/Tools/Reapr_1...
2107 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C...= do{ local $/; }; chomp $in; print $in; for my $p1 ( 1 .. le...ess substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1 };...*2; my $ed=($st+$sLen)-1; print "$st\t$ed\t$sLen\t$val\n";...2107 days ago
