Dual index barcode demultiplex issue
Hello,
Following are the list of dual indexed illumina libraries we have used for illumina run.But we were not able demultiplex the data by using the barcodes.Because 99% of the data going as undetermined.
Index1 —— Index2 ( case1 )
ATGAGC —- TGAACCTT
ATTCCT —- TGAACCTT
CAAAAG —- TGAACCTT
CAACTA —- TGAACCTT
CACCGG —- TGAACCTT
There after we tried demultiplex with reverse compliment of index 2 and No changes in Index1(list are below ).This worked well and able to determine 98% of the data.The question is why the demultiplex only worked with reverse compliment of index2 and not in the case1(without reverse compliment)
Index1 —— Index2 (reverse compliment)
ATGAGC —- AAGGTTCA
ATTCCT —- AAGGTTCA
CAAAAG —- AAGGTTCA
CAACTA —- AAGGTTCA
CACCGG —- AAGGTTCA
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