Results for "IT"
Bio-Scripts
Perl subroutine to read genome/reads fasta file !
...$file:$!\n"); while(){ chomp; if($_ =~ /^>/){ if(defined $id && defined $seq){ $map{$id} = $seq; $seq=""; } ($id) = split(' ',$_); $id=~s/>//; }...2192 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqTyp..._target: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity....6.6/trinity_out_dir/read_partitions/Fb_0/CBin_47 Monday, Jul....6.6/trinity_out_dir/read_partitions/Fb_0/CBin_197 Monday, Ju...
2186 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --hel...CE" PROCESSING Read Splitting Seque...Applied to spots when --split-spot is not...aligned-region Filter by position on genome. Name can...present it is placed in *.fastq Biologic...
2185 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, '2184 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1...▓▓░ Transrate v1.0.3 by Richard Smith-Unna, Chris Boursnell, Rob P...Show some example commands with explanations ➜ BorisTrinit...orisTrinityAssembly/transrateSTAT/Trinity [ INFO] 2018-07-13 14:54:21...
2182 days ago
- # list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5daup/download", "ERR458494":"https://osf.io/8rvh5/download",...
1575 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git C...orechop copying porechop/__init__.py -> build/lib/porechop C...urbe/anaconda3/lib/python3.6/site-packages/porechop/adapters.p...(incompatible with --output) --barcode_thres...2165 days ago
- ...k WadinetaGapFilled.gapfilled.iteration1.fa" echo "[REAPR p...s WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam o...r WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam o...5 WadinetaGapFilled.gapfilled.iteration1.fa /home/urbe/DATA/Or...
2158 days ago
- ➜ Tools git:(master) ✗ git clone https://github.com/Nextomics/nextsv.git...CMakeFiles/zlibstatic.dir/gzwrite.o [ 9%] Building C object...[-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(...Sniffles finished ➜ nextsv git:(master) ✗
2157 days ago
Install Python locally on shared Linux server !
...nload the python source and extract it mkdir ~/python cd ~...hen I compiled the source following its guideline ./configure --p...output of make command, by default it is in the /usr/local/ and we...run this command: which python #it should show you the path to t...2157 days ago
