Results for "pe"
Bio-Scripts
Long reads mapper bash script !
...LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/...$2 longReads=$3 thread=$4 readsType=$5 if [ $# -lt 5 ]; then...provided" echo "#USAGE: runMapper.sh minimap2 ref.fa reads.fa/...t.sam else echo "LAMSA:Please specify reads type: ont, pacbio"...2179 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(defined $id && de...2190 days ago
- ..._read_normalization.pl --seqType fq --JM 250G --max_cov 50 --...--sorted > pairs.K25.stats -opening left.fa.K25.stats.sort -...nning CMD: bash -c " set -o pipefail;/home/urbe/anaconda3/bin/...y 1G --run_as_paired --seqType fa --trinity_complete --full_...
2184 days ago
- ...rs Applied to the full spot independently...NC_000001.10) or file specific name (ex:...for SOLiD),"cskey" may be specified for...
2183 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, '2182 days ago
- ...(default: info) --install-deps= Install any missing dependencies. One of [ref] --ex...with orf 61028 [ INFO] 2018-07-13 14:54:34 : mean orf percent 61.07 [ IN...
2179 days ago
- ...study rule download_all: input: expand("rnaseq/raw_data/{sample}.fq.gz", sample=SAMPLES) # rule to download each individual file specified in sample_links rule d...
1573 days ago
Installing Porechop on Ubuntu !
...copying porechop/cpp_function_wrappers.py -> build/lib/porechop c...-fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -c -o por...build/lib/porechop/cpp_function_wrappers.py -> /home/urbe/anaconda3/...A read must have at least this percent identity to a...2162 days ago
- ...ration1.fa" echo "[REAPR pipeline] Running preprocess" ech...ineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 01.sta...unning reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools..._____________________ test perfectmap " reapr perfect...
2155 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 $in; print $in; for my...2155 days ago
