From the stats-dada2 output i get that the % input non-chimeric is 50-60% is this percentage OK? Or should I get >80%? Please let me know.
Also I have jejunum, ileum, cecum and colon samples and while the last two have at least 10 phyla the jejunum and ileum samples only have 2 to 3 phyla? Is this possible? I would expect more phyla to be seen.
Could this be due to the % input non chimeric?
Thank you very much, Paula.
For some datasets it is ok, for others - not so good... It depends on a lot of factors. Were primers removed before dada2?
First of all, you need to inquire on which step you lost most of the missing reads:
- Filtering. Check the quality plots. If they looks bad than it is not surprising that a lot of reads were filtered out. If quality looks ok, try to set a lower values fro truncation and see if it will help.
- Merging. Probably overlapping region is too short. Try to set higher truncation values and/or decrease minimum ovelap parameter in dada2.
- Chimeras removal. High % of chimeras can be caused by primers still atached to the reads. Primers removal will decreased it.
Please, always provide detailed information. In such way moderators or other forum members will be able to help you faster and more effectively.