Results for "C"
Bio-Scripts
➜ Tools git:(master) ✗ git clone https://github.com/Nextomics/nextsv.git Clon...piler ABI info - done -- Detecting CXX compile features --...quence.cpp.o [ 27%] Building CXX object lib/bamtools-2.3.0/s...pp.o [ 64%] Building CXX object src/CMakeFiles/sniffles.dir/...2126 days ago
Install Python locally on shared Linux server !
#Install python to local directory #Firstly, I create a folder in my home directory, download the python sour...find ~/python -type d | xargs chmod 0755 cd Python-2.7.11...t the #related output of make command, by default it is in th...#able to see a new python. To check, run this command: whi...2125 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqf...); open FILE, $idsfile; while() { chomp; $ids{$_} += 1; } close FILE; local $/ = "\n>"; # read by FAST...print ">$id\n$seq\n"; } } close FASTA;...2123 days ago
Installing Busco version 4.0.6
...base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 Collecting package metadata (re...h516909a_2 777 KB bioconda r-assertthat-0.2.1...tf8-1.1.4 | r36hcdcec82_1003 161 KB co...3f_1003 r-nlme conda-forge/linux-64::r-nlme-3....1480 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/release...SDisk/SNP/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar --help...------------------- Diagnostics and Quality Control:...a single file GatherTranches...
2103 days ago
- ...Updating Oh My Zsh remote: Counting objects: 484, done. remote: Compre...| 2 +- plugins/extract/extract.plugin.zsh...| 17 +++-- plugins/per-directory-history/README.md...lugins/jenv/jenv.plugin.zsh create mode 100644 plugins/swif...
2102 days ago
Perl script to extract a sequence from multifasta with range !
...fastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-l...n` parameter not provided\n"; { local $/=">"; while() {...my $seqlen = length join "", @chunk; print ">$_" if(...2093 days ago
Perl script to break the contigs by 'N'
...ta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff");...fasta->next_seq() ) { #gets contig id my $contig = $seqob...#Searches for NNNNN regions (scaffold breaks) #Hash nregion...hout Ns are in @regions my $cont=1; my $laststart=1; if...2090 days ago
- library(vcfR) # Input the files. vcf
2087 days ago
#Install older version of R Packages !
#Install older version of R Packages ! require(devtools) install_version("IdeoViz", version = "0.9.1", repos = "http://cran.us.r-project.org")2087 days ago
