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Bio-Scripts
Long reads mapper bash script !
...longReads=$3 thread=$4 readsType=$5 if [ $# -lt 5 ]; then echo "No or less arguments provided"...refFasta -d $longReads -t $thread -o $fileName.out.sam else echo "Unknown mapper name and parameter !...2178 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(){ chomp; if($_ =~ /^>/){ if(de...2188 days ago
- ...IG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq' ];...------------ In silico Read Normalization ------------------...IG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq >> right.fa...IG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K2...
2182 days ago
- ...Applied to spots when --split-spot is not...lter Filter used in early 1000 Genomes data: no...reads and above are ignored. -G|--spot-group...
2181 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 $fh, '2180 days ago
- ...Patro, Julian Hibberd, and Steve Kelly DESCRIPTION: Analyse a de-novo transcriptome assembly usin...:54:34 : Contig metrics done in 13 seconds [ INFO] 2018-07-13 14:54:34 : No reads provided, skipping read...
2178 days ago
Installing Porechop on Ubuntu !
...copying build/lib/porechop/nanopore_read.py -> /home/urbe/ana...n3.6/site-packages/porechop/nanopore_read.py to nanopore_read....or FASTQ of trimmed reads (if not s...pairs will not be outputted (default: 1000)...2161 days ago
- ...reapr stats -p /home/urbe/Tools/Reapr_1.0.18/Wadineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 0...reapr stats -p /home/urbe/Tools/Reapr_1.0.18/Wadineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 0...
2154 days ago
- ...6bbe1fd22a2f/argparse-1.4.0-py2.py3-none-any.whl Installing collect...ing CXX compile features - done -- No build type specified. Using '...bject src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o /home/u...r/Cluster_SVs.cpp:87:22: warning: ignoring return value of ‘int syst...
2154 days ago
Install Python locally on shared Linux server !
...--prefix=$HOME/python make && make install #Notice the prefix option, it is...e our own #customized directory. #Here comes another important step. By the de...command to install pip as a local user wget --no-check-certificate https://boo...2153 days ago
