Ion torrent .sff file to fasta error


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.

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?


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.