Ion torrent .sff file to fasta error

Commands in mothur
1

Hi

I am trying to get fasta files from .sff files. So i am using the two commands below to get the files. I see the temp files made but then they vanis and end up with a huge scrap file. I have previously used the .sff file and same commands (below) to get the fasta files.

sffinfo(sff=./ion.sff)
trim.seqs(fasta=./ion.fasta, oligos=./ion.oligos, qfile=./ion.qual, maxambig=0, maxhomop=5, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=30, qwindowsize=50, allfiles=T, processors=4)

What am i goofing up. Is it the oligo file?

Thanks

2

No, its probably the quality file. IonTorrent (assuming that’s what ion stands for) gives very low quality scores. We’re working to figure out what they mean. Unless you co-sequenced a mock community it’s hard to say what to suggest.

Also, you can look at the scrap.fasta file to see why things got scrapped by looking at the characters after the | character.

Pat