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Defining transcribed regions using RNA-seq

• url: "http://www.nature.com/nprot/journal/v5/n2/full/nprot.2009.229.html"

Yeast culture

1

• process: "Preculture of S. pombe"
• input: "yeast cells picked from a YES agar plate"

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@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix uo: <http://purl.obolibrary.org/obo/> .

<http://purl.jp/bio/01/quanto/resource/DRR047105_fastqc> a <http://purl.jp/bio/01/quanto/ontology/sos#SequenceStatisticsReport>;
   <http://purl.jp/bio/01/quanto/ontology/sos#encoding> "Sanger / Illumina 1.9";
   <http://purl.jp/bio/01/quanto/ontology/sos#fastqcVersion> "0.11.3";
   <http://purl.jp/bio/01/quanto/ontology/sos#fileType> "Conventional base calls";

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@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix uo: <http://purl.obolibrary.org/obo/> .

<http://purl.jp/bio/01/quanto/resource/QNTDRR000001_1> a <http://purl.jp/bio/01/quanto/ontology/sos#SequenceStatisticsReport>;
   <http://purl.jp/bio/01/quanto/ontology/sos#encoding> "Sanger / Illumina 1.9";
   <http://purl.jp/bio/01/quanto/ontology/sos#fastqcVersion> "0.11.3";
   <http://purl.jp/bio/01/quanto/ontology/sos#fileType> "Conventional base calls";

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# :)

if __FILE__ == $0
  # Arguments
  input_fastq = ARGV[0]
  trimming_sequence = ARGV[1]
  head_or_tail = ARGV[2] || "HEAD"
  
  # Load data
  data = open(input_fastq).readlines

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# :)

require 'benchmark'
include Benchmark

def find_median_by_sorting(v)
  sorted = v.sort
  quot = sorted.size / 2
  if !sorted.size.even?
    sorted[quot]

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  %   cumulative   self              self     total
 time   seconds   seconds    calls  ms/call  ms/call  name
629.76 61567.87  61567.87       51 1207213.14 1656235.29  Array#sort
234.24 84468.00  22900.13 1089421708     0.02     0.02  Float#<=>
100.00 94244.16   9776.16       64 152752.50 152752.50  Thread#value
  1.76 94416.63    172.47      151  1142.19  1142.19  IO#close
  1.75 94587.49    170.86      203   841.67   841.67  File#initialize
  1.46 94730.61    143.12     4084    35.04    35.04  IO#read
  0.49 94778.91     48.30       50   966.00   966.00  Zlib::Inflate#inflate
  0.42 94819.79     40.88      384   106.46   106.46  IO#write

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@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix uo: <http://purl.obolibrary.org/obo/> .

<http://purl.jp/bio/01/quanto/resource/QNTDRR000001_1> a <http://purl.jp/bio/01/quanto/ontology/sos#SequenceStatisticsReport>;
   <http://purl.jp/bio/01/quanto/ontology/sos#encoding> "Sanger / Illumina 1.9";
   <http://purl.jp/bio/01/quanto/ontology/sos#fastqcVersion> "0.11.3";
   <http://purl.jp/bio/01/quanto/ontology/sos#fileType> "Conventional base calls";

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[
  {
    "@id": "http://me.com/data/QNTDRR000001_1",
    "http://me.com/sos#encoding": [
      {
        "@type": "http://www.w3.org/2001/XMLSchema#string",
        "@value": "Sanger / Illumina 1.9"
      }
    ],
    "http://me.com/sos#fileType": [

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RDFizing FastQC/Quanto data

Thanks to skwsm-san!

Original FastQC data used for modeling is embedded here.

Model for modules with data matrix

<Quanto Record> a :SequenceStatisticsReport .

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// Thanks Amit! http://www.labnol.org/internet/auto-confirmation-emails/28386/
/* Send Confirmation Email with Google Forms */

function Initialize() {
  var triggers = ScriptApp.getProjectTriggers();
  for (var i in triggers) {
    ScriptApp.deleteTrigger(triggers[i]);
  }

  ScriptApp.newTrigger("SendConfirmationMail")