Design Your Run

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

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

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