BOL

Results for "single-cell mRNA sequencing"

Bio-Scripts

• • Radha Agarkar@radhaagarkar

  

  Parse a Fasta file with Perl

  #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "

  2910 days ago

• • Radha Agarkar@radhaagarkar

  

  Needleman-Wunsch Algorithm in Perl

  #!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needleman-Wu...

  2902 days ago

• • EagleEye@santhilalsubhash

  

  Calculate confidence interval for multiple columns in a matrix (table) using R function CI_normal and CI_tdist

  #USAGE: CI_normal(matrix[,c(x:y)],97.5) - multiple column from a normal distribution #USAGE: CI_tdist(matrix[,c(x:y)],97.5) - multiple column from a t distribution #USA...

  2868 days ago

• • Jit@jit.aber

  

  Perl script to convert GFF 2 FASTA !

  #!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; #...fasta parsed\n"); ### Second, parse the GFF3 my %CDS; my %CDNA; my $mRNA_name;...

  2135 days ago

• • Jit@jit.aber

  

  Running Trinity on RNA-seq !

  ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_c...

  2123 days ago

• • Jit@jit.aber

  

  Fastq-dump for SRA download

  ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...] ./fastq-dump [options] INPUT -A|--accession Replaces accession deriv...

  2122 days ago

• • Jit@jit.aber

  

  Downloading GATK !

  ...Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapte...Collect whole genome sequencing-related metrics. Colle...ed allele fractions in pooled sequencing CalculateGenotypePosteri...

  2071 days ago

• • Jit@jit.aber

  

  Installing pb-assembly on Linux !

  [jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles --------------------------------------------...

  2030 days ago

• • Jit@jit.aber

  

  Installing nupack3.0.6

  #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupack3.0.6 ➜ nupack3.0.6 git:(master) ✗ make make -C src/ make[1]: Entering directory '/home/urbe...

  2022 days ago

• • Jit@jit.aber

  

  Bash script to download SRA file !

  #We can use the sratoolkit to directly pull the sequence data (in paired FASTQ form...p is in the SRA toolkit. It allows directly downloading data from a particular sequencing run ID fastq-dump --split-...

  1555 days ago

• « Previous
• 1
• 2
• 3
• Next »