Hi, Guys
I am new to NGS. We've been trying to do whole genome bisulfite sequencing on Nextseq 500 for a few times with 2 samples.
We always encountered the same problem. After demultiplexing, there is about 50% of unknown index reads (most of them are "GGGGG" and "NNNNNN") . According to other centers using exact same kit and machine, they do not have any problems with adapters and indexes. And we always use single-use illumina kit and reagent for each run. So we do not know what happens.
We ve also tried to map read1 and read2 (with unknown barcodes). The alignment of read1 is quite good (90% aligniable), but reads2 is not good (~40%).
We used custom primer for read1 and illumina primers for read2 and index.
Many thanks in advance!
Roger
I am new to NGS. We've been trying to do whole genome bisulfite sequencing on Nextseq 500 for a few times with 2 samples.
We always encountered the same problem. After demultiplexing, there is about 50% of unknown index reads (most of them are "GGGGG" and "NNNNNN") . According to other centers using exact same kit and machine, they do not have any problems with adapters and indexes. And we always use single-use illumina kit and reagent for each run. So we do not know what happens.
We ve also tried to map read1 and read2 (with unknown barcodes). The alignment of read1 is quite good (90% aligniable), but reads2 is not good (~40%).
We used custom primer for read1 and illumina primers for read2 and index.
Many thanks in advance!
Roger
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