Designing Your Run

Designing Your Run

To ensure a successful sequencing run, the sample must meet sufficient purity, quantity, and quality standards. Your submitted samples will be checked to meet these standards, and this QC assessment is included in the library prep price for each submitted sample that goes on to be prepared for sequencing. If the submitted sample needs to be improved, however, we are happy to work with the investigator to reach the necessary standards. Any additional QC assessment will be charged according to the current posted pricing sheet. 

Important Considerations

Consider the following when designing your run.

Read Type 

  • Single End Reads (SE)
    • Usually sufficient for expression studies (with an available reference)
    • RNASeq profiling
  • Paired End Reads (PE)
    • Used for additional positional information during de novo genome assembly
    • Easier to resolve structural rearrangements (such as SNPs)
    • Assists discovering isoforms
    • Assists with determining epigenetic modifications

Read Length

Longer reads give more information on relative position within a genome 

  • 75 cycles - sufficient to map reads to a genome or for RNASeq expression studies with an available reference
  • 150 cycles - chosen for genome or transcriptome studies that require high amounts of coverage

Coverage Depth

  • DNA - commonly determined by recent scientific journals pertaining to the research study
    • DNA Resequencing (reference is available) 30X-50X
    • DNA de novo assembly 50X-100X
    • SNP/Rearrangement Analysis 10X-30X
    • Exome Seq 100X-200X
    • ChIPSeq 10X-40X
  • RNA - more difficult to determine because transcripts are expressed at different levels
    • Considerations:
      • transcriptome complexity
      • amount of alternate expression
      • 3' associated biases
      • range of expression levels of transcripts