Results for "PE"
Bio-Scripts
...ting CXX compile features - done -- No build type specified. Using 'release' -- Tr...CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o [ 42%] Building CXX...ffles [ 78%] Built target sniffles Scanning dependencies of target sniffles-de...2145 days ago
Install Python locally on shared Linux server !
...gz tar zxfv Python-2.7.11.tgz find ~/python -type d | xargs chmod 0755 cd Pyth...this to work. The value of prefix option is to specify where to put the #related...and login again for the environment to update properly. At this point, you should...2145 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() {...E; local $/ = "\n>"; # read by FASTA record open FASTA, $seqfile; while () {...2143 days ago
Installing Busco version 4.0.6
...4.1 MB conda-forge openblas-0.2.20 |...11 KB bioconda perl-extutils-cbuilder-0.280230|...metis-5.1.0-he1b5a44_1005 openblas conda-forge/li...following packages will be SUPERSEDED by a higher-priority ch...1500 days ago
- ...tool Configuration File Specification --gatk-config...sequencing data into an unmapped SAM or BAM file. MarkIl...r BAM file. CollectIndependentReplicateMetrics (Picard)...gar (Picard) (BETA Tool) (Experimental) Examines aligned rec...
2122 days ago
- ...lib/prompt_info_functions.zsh | 2 +- lib/spectrum.zsh...ins/pass/_pass | 17 +++-- plugins/per-directory-history/README.md...
2121 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift or die "Error: `minlen` parame...2113 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict;...[0].parts.fasta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff...eq = uc $seq; #now all bases are in uppercase #Searches for NNNNN...for this loop, but its less memory expensive than regular expressions...2109 days ago
- library(vcfR) # Input the files. vcf
2107 days ago
Generate simulated polyploid genome !
...msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3...na paired-end reads sim_reads --depth 50 toyheterozygous3percent.fasta > toyheterozygous3...2100 days ago
