How to work with single and paired reads

Commands in mothur
1

I’m reproducing a study that has fastq files from single and paired reads. I know how to execute mothur using paired reads creating the stability file, but I don’t know how to include the single ones.
Does anyone knows?

Thanks!

2

Honestly, it’s pretty hard to combine the analyses. The error rate for the single read data will be much higher and will lead to an artificially inflated level of diversity. You might try using trim.seqs, but I’m not sure what parameters to suggest using for those single reads.

Pat

3

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.