Low quality of NGS SNP analysis panel

Question

[kate-nelis]

Hi, this is the first time I'm dealing with such an analysis and I have some questions. I've received a few files from an SNP IonTorrent panel, but their quality is rather low when I put them through fastqc. It's the first time I'm dealing with such data, and have no idea how to approach it. The sequence duplication levels are high and there are overrepresented sequences

When I filter them using fastp, only a small percentage (or none at all) make it through. What could be the reason of such a result?

Answer 1

[Prash]

Hi Kate Your data looks normal for Ion Torrent and it is expected. Please check with the service provider the libprep methods and normalization steps they have followed. The barcode adaptors for IonTorrent Xpress are specifically designed and validated for optimal performance, but sometimes they vary

Hope this helps Prash