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 m (→Method) |
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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)
- The index of the list corresponds to hexamer sequence using a quaternary numeral system where A = 0, T = 1, C = 2, G = 3
- Output is a \n separated list of length 4096
- 64 hexamers with 10,000+ occurrences in mRNA and 0 in rRNA
- Use perl script to convert the index number to hexamer sequence