What is the extra 1 base in the Truseq adapter file (TruSeq3-PE-2.fa)

[wjlim]

I found that the adapter sequence you guys provided have the extra 1base compared with Illumina protocol.

TruSeq3-PE-2.fa

PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
PE1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
PE2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
PE2_rc
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Read1
AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Read2
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

What is purpose of the extra base?

[mmokrejs]

The sequences provided are correct, IMO.

For the first one I see these variants exist indeed:

>TruSeq3/1 http://seqanswers.com/forums/showthread.php?t=40926 aka rc_Rd2SP is followed by a barcode and then atctcgtatgccgtcttctgcttg
aGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>floppy_end_adapter_right (HingeRegion+R2_SequencingPrimer+P7_Adapter_Core_on_FC) can be followed by a barcode on 3'-end
aGATCGGAAGAGCACACGTCTGAACTCCAGTCACatctcgtatgccgtcttctgcttg
>TruSeq_Adapter+CAGATC+P7_Adapter_Core_on_FC+polyA+polyG
aGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNatctcgtatgccgtcttctgcttgAAAAAAAAAAGGGGGGG

For the second you mention I also see:

>TruSeq_Adapter_Index_CTTGTA in R1 reads
aGATCGGAAGAGCACACGTCTGAACTCCAGTCACcttgtaATCTCGTATGCCGTCTTCTGCTTG
>TruSeq_Adapter_Index_CTTGTA+polyA in R1 reads2
aGATCGGAAGAGCACACGTCTGAACTCCAGTCACcttgtaATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA

It is always good to inspect your reads on both end and learn, how they differ between the sampels, where are the barcodes placed and whether you specify a proper command to trim them away.