Matt:LabNotes/2014-5-14: Difference between revisions

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>Mzcai
(Created page with "==Designing Hexamer Oligo Primers for RT - Enriching mRNA Rolonies== ===Method=== *Download mRNA, rRNA, and MT-rRNA sequences from biomart in fasta format **Ensembl Genes 75 ...")
 
>Mzcai
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**Homo sapiens genes (GRCh37.p13) Dataset
**Homo sapiens genes (GRCh37.p13) Dataset
**Filter with Gene type: protein_coding, rRNA, MT-rRNA
**Filter with Gene type: protein_coding, rRNA, MT-rRNA
***92,169 protein-coding transcripts
***568 rRNA transcripts
**Attributes: Sequences of Unspliced (Transcript)
**Attributes: Sequences of Unspliced (Transcript)



Revision as of 23:39, 16 May 2014

Designing Hexamer Oligo Primers for RT - Enriching mRNA Rolonies

Method

  • Download mRNA, rRNA, and MT-rRNA sequences from biomart in fasta format
    • Ensembl Genes 75 Database
    • Homo sapiens genes (GRCh37.p13) Dataset
    • Filter with Gene type: protein_coding, rRNA, MT-rRNA
      • 92,169 protein-coding transcripts
      • 568 rRNA transcripts
    • Attributes: Sequences of Unspliced (Transcript)
  • Use perl script to count number of instances each of the 4096 hexamer sequences appeared
    • Output is a \n separated list of length 4096
      • The index of the list corresponds to hexamer sequence using a quaternary numeral system where A = 0, T = 1, C = 2, G = 3
        • e.g. AAAAAA = 000000 = 0 (or the first number in the list)
        • e.g. AAAAAT = 000001 = 1 (or the second number)
        • e.g. AAGAAA = 001000 = 192 (or the 193rd number)
  • 64 hexamers with 10,000+ occurrences in mRNA and 0 in rRNA
  • Use perl script to convert the index number to hexamer sequence