1. Background
  2. Data Collection Methods
  3. Data Quality Control
  4. Summary

Adapted from Martin and Wang (2011). bp = base pairs

Sequencing

Factors to consider before sequencing a sample (Martin and Wang, 2011 ):

  1. Choice of sequencing platform/instrument.
    1. Illumina IG or Applied Biosystems SOLiD for large and complex transcriptomes.
    2. Roche 454 Life Science produces longer reads and can be used alone for small transcriptomes.
  2. Sequencing read length. For transcriptome assembly, longer read lengths are preferred. Problems posed by short reads may be alleviated by a paired-end sequencing protocol.
  3. Single-end or paired-end sequencing.
    1. Paired-end sequencing involves sequencing 75 to 150 bp from both ends of short cDNA fragments (100 - 250 bp).
    2. Overlapping fragments can be computationally joined to produce a longer read.