245
by the quality filters for being polyclonal, having low read
quality, or the result of primer dimer.
- These reports are used to evaluate the quality of the Ion
Torrent PGM run. A good quality run has at least 30% ISP
loading and 30% usable reads. - The data from the sequencing runs can be analyzed using the
Torrent Suite analysis pipeline, which includes raw sequencing
data processing (DAT processing), splitting of the reads
according to the barcode for the individual sample output
sequence, classification, signal processing, base calling, read fil-
tering, adapter trimming, and alignment quality control.
4 Notes
- If you are using a DNA panel with two primer pools, set up
two 10-μL amplification reactions, then combine them after
target amplification to give a volume of 20 μL. - Cycle number recommendations in the table are based on
10-ng DNA input. Cycle number can be increased when input
material quality or quantity is questionable. - Residual ethanol drops inhibit library amplification. If needed,
centrifuge the plate and remove remaining ethanol before air-
Fig. 5 Chip Minifuge for centrifugation of chip. It enables effective and efficient sample loading. The minifuge
quickly accelerates to maximum speed and stops quickly
Next Generation Sequencing and Esophageal Adenocarcinoma