NovaSeq data analysis

Question

[anu014]

Hello Biostars!

Hope you all are doing well :)

Today, it's something brand new analysis I'm required to do. It's to analyze the NovaSeq data. Can anyone suggest me some tools to start with?

Few things I've noticed. There is significant difference between regular FASTQ from HiSeq and one from NovaSeq (due to difference between quality table used by both, ASCII for HiSeq and only 4 qualities in NovaSeq). So Trimgalore won't work. How to check quality for the data & trim it?

Please help me out. Thank you

[Devon Ryan]

What kind of data are we talking about? RNA-seq, WGS, ChIP-seq, etc.?

[anu014]

Hi Devon. Sorry for the late reply. It's metagenomics data (shortgun sequencing; 2 X 150 paired end data).

Answer 1

[GenoMax]

Illumina switched to using binned Q scores for data (see white paper and specific app note for NovaSeq). There should be no significant difference between data from HiSeq/NovaSeq as far as analysis is concerned.