important considerations


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


transcriptome complexity

amount of alternate expression

3' associated biases

range of expression levels of transcripts