Dear Sr Developer,
I got an advising to reduce the my Illumina dataset by filtrate those and take about 30% of the sequences in order to run the ITS protocol.
For this I used the software https://usegalaxy.org/root within this method:
NGS: QC and manipulation: Filter by quality:
Quality cut-off value - 30
Percent of bases in sequence that must have quality equal to / higher than cut-off value - 90
It means that:
percent = 90 and cut-off = 30 - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30).
From now on could you please guide me how to run the metagenome analysis with the galaxy? I would like to get the alfadiversity, relative abundande and OTU data.
Thanks in advance,