I have MiSeq data (fastq.gz format) that I am trying to preprocess for microbiome analyses.
The workflow I've come up with is the following:
- Join paired end reads
- Trim sequences to remove primers & barcodes
- Quality Filter
I have tools to do numbers 3 & 4 above (Qiime or mothur). But I can't seem to get anything to work for part 1 & 2.
I have two questions:
1) Is the workflow above in the correct order?
2) Is there a semi-straight forward tool (decent documentation/workflow examples) to join my paired reads and & trim sequences? So far, I've tried using fastqjoin, but haven't been able to figure out how to use it. Mothur has a trim.seqs function, but I've been having issues with that, too.
If these are the best tools, I'll start a different topic for trying to get them to work. I just don't want to spend hours trying to get something to work if it isn't the best way for a beginner to do it. Thanks in advance.