So I got the raw data with mixed of both forward and reverse sequences in ffastq and rfastq files. It would be fine to us since we could make.contigs and trim.seqs later. But the problem of this one is that I can’t make.contigs this time because one file has 2,300,000 reads while the other has 2,000,400 reads (not exact number, but you get the gist). Mothur said it can’t make contigs and suggested me to make.list and get.seqs first. So I did:
make.list(fastq=xx_forward.fastq) and get accnos file. Then I get.seq(accnos=xx_forward.accnos, fastq=xx_reverse.fastq). then fastq.info(fastq=current) to get xx_reverse.pick.fasta. To make sure I get it thoroughly, I did make.list(fastq=xx_reverse.fastq), then get.seq(accnos=xx_reverse.accnos, fastq=xx_forward.fastq). and fastq.info(fastq=current) and get xx_forward.pick.fasta.
Then I make.contigs(ffasta=xx_forward.pick.fasta, rfasta=xx_reverse.pick.fasta) but I got the error saying mismatch name and ended up with 0kb file.
I even did get.seqs(accnos=xx_reverse.accnos, fasta=xx_forward.pick.fasta) and get xx_forward.pick.pick.fasta and the same way got xx_reverse.pick.pick.fasta. Then I tried make.contigs. Still the same error as mismatched name and no sequence in the file.
I’m sure I’ve missed something here. Any suggestion would be appreciated.