Sequencing requirements for common applications. The figures provided are intended as guidelines to help with the planning of experiments.

RNA sequencing

Indicative number of reads requirements
Analysis typeNumber of fragments (reads) per sample Number of samples per lane (HiSeq4000)Number of samples per flowcell (NextSeq500)References
 Differential expression profiling  10-25M  12 for 25M reads  16 for 50M reads  Liu Y. et al., 2014; ENCODE 2011 RNA-Seq
 Total RNA  50M  6  8  
 Alternative splicing  50-100M  3 for 100M reads  4 for 100M reads  Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
 Allele specific expression  50-100M  for 100M reads  4 for 100M reads  Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
 De novo assembly  >100M  >3  >4  Liu Y. et al., 2013; ENCODE 2011 RNA-Seq
 Small RNA (differential expression)*  1-2M  up to 135   up to 180  Metpally RPR et al., 2013Campbell et al., 2015
 Small RNA (discovery)*  5-8M  up to 37   up to 50  Metpally RPR et al., 2013Campbell et al., 2015

The figures provided are estimates based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors. Sequencing prices (behind login)

For smallRNA sequencing the MiSeq platform is adequate for up to 11 samples for differential expression.

Summary of the table's contents

RNA interactions

Indicative number of reads requirements
Analysis typeNumber of fragments (reads) per sampleNumber of samples per lane (HiSeq4000)MiSeqReferences
 iCLIP  5-15M  20 - 60    up to 4  Sugimoto Y. et al., 2012Rogelj B. et al., 2012
 CLIP-Seq  10-40M  7 - 30   up to 2  Cho J. et al., 2012; Eom T. et al., 2013Sugimoto Y. et al., 2012
 PAR-CLIP  5-15M  20 - 60   up to 4  Rogelj B. et al., 2012
 RIP-Seq  5-20M  15 - 20   up to for  Lu Z. et al., 2014

The figures provided are estimates based on on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors. Sequencing prices (behind login)

For smallRNA sequencing the MiSeq platform is adequate for up to 11 samples for differential expression.

Summary of the table's contents

Single cell genomics

Indicative number of reads requirements
ApplicationNumber of reads per cellNumber of cells per lane (HiSeq4000)Number of cells per flowcell (NextSeq500) 
 10X Genomics 3' RNA-seq  50K  6K  8K  
 10X Genomics 5' V(D)J repertoire, human T cells  5K  60K  80K  
         
The figures provided are estimates based on on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors. One library prep with the Single Cell Chromium can capture up to 10K cells. Sequencing prices (behind login)
Summary of the table's contents

Chromatin structure and accessibility

Indicative number of reads requirements
ApplicationNumber of readsNumber of samples per lane (HiSeq4000)Number of samples per lane (NextSeq500)References
 Hi-C  100M  3   4   Belton, J.M et al., 2012
 4C (Circularised Chromosome Cofirmation Capture)  1 - 5M  60   80   van de Weken, H.J.G. et al., 2012

 5C (Chromosome Carbon Capture Carbon Copy)

 15 - 25M   12   33  Sanyal A. et al., 2012

ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing)

 15 - 20M   15   20  Zhang, J. et al., 2012
 FAIRE-Seq  25 - 55M   5   7  ENCODE 2011 Genome; Landt et al., 2012
 DNAse 1-Seq  25 - 55M   5   7  Landt et al., 2012
 ATAC-seq  25 - 50M      ENCODE project
         
The figures provided are estimates based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors. Sequencing prices (behind login)

Epigenetics (ChIP and Methylation)

Indicative number of reads or coverage requirements
Analysis typeCoverage or number of readsNumber of samples per lane (HiSeq4000)Number of samples per lane (NextSeq500)References
 ChIP-seq (sharp peaks)  10-14M reads    21 - 30   28 - 40  Rozowsky et al., 2009; ENCODE 2011 Genome
 ChIP-seq (broad marks)  20-40M reads    7 - 15    10 - 20    Landt et al., 2012; ENCODE 2011 Genome
 CAP-Seq  >20M reads   6   9  Long, H.K. et al., 2013
 MeDIP-Seq  60M reads   5   6  Taiwo, O. et al., 2012
 RRBS (Reduced Representation Bisulfite Sequencing)  10X coverage of genome   2   3  ENCODE 2011 Genome
 Bisulfite-Seq  5-15X to 30X coverage   1 - 2   2 - 3  Ziller, M.J et al., 2015; Epigenomics Road Map
The figures provided are estimates based on on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors. Sequencing prices (behind login)
Summary of the table's contents

Whole genome sequencing

Indicative coverage requirements
Analysis typeCoverageNumber of lanes per sampls (HiSeq4000 - 150PE)Number of lanes per sampls (NextSeq500 - 150PE)References
 Homozygous SNVs  15X  1  2  Bentley et al., 2008
 Heterozygous SNVs  33X  2  1  Bentley et al., 2008
 INDELs  60X  3  2  Feng et al., 2014
 Genotype calls  35X  2  1  Ajay et al., 2011
 CNV  1-8X  up to 25 samples per lane  up to 32 samples per lane  Xie et al., 2009Medvedev at al., 2010
The figures provided are estimates based on on performance specifications provided by the manufacturer and 10% duplicates, Output may vary depending on sample quality, cluster density and other experimental factors. Sequencing prices (behind login)
Summary of the table's contents