adapter-seq.md

3RAD Adapter Sequences

iTru5-8N Primer

5' AAT GAT ACG GCG ACC ACC GAG ATC TAC AC (N:25 25 25 25)(N)(N)(N)(N)(N)(N)(N) ACA CTC TTT CCC TA*C 3'

Read 1 P7 Primr

5' CAA GCA GAA GAC GGC ATA CGA GA 3'

Read 2 P5 Primer

5' AAT GAT ACG GCG ACC ACC GAG AT 3'

Read 1 restriction enzymes

XbaI

5' T/C T A G A 3'
3' A G A T C/T 5'

MspI

5' C/C G G 3'
3' G G C/C 5'

Read 2 restriction enzymes

EcoRI

5' G/A A T T C 3'
3' C T T A A/G 5'

BamHI

5' G/G A T C C 3'
3' C C T A G/G 5'

Adapter dimer restriction enzymes

NheI

Cuts dimers formed by XbaI adapters
5' G/C T A G C 3'
3' C G A T C/G 5'

ClaI

Cuts dimers formed by MspI adapters
5' A/T C G A T 3'
3' T A G C T/A 5'

Illumina TrueSeq HT Dual Index Adapter Sequence

Read 1

Full Adapter Sequence

5' GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG 3'

Read 2

Full Adapter Sequence

5' AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3'

Adapter Length

Read 1

62 + 8 = 70 bp

Read 2

57 + 8 = 65 bp

Total

70 + 65 = 135 bp