Analysing Ion Torrent Data

Commands in mothur
1

Hi,

I have sequenced using the ION TORRENT, and they sent to me a sff file. I found the tutorial “Ion Torrent sequence analysis using Mothur” on mothur website. However, when I use the sffinfo command I receive the following message:
mothur > sffinfo(sff=eliana.sff)

Extracting info from eliana.sff …
Version is not supported, only support version 0001.
It took 0 secs to extract 0.
Output File Names:
eliana.fasta
eliana.qual
eliana.flow


All files are empty. I tried using mothur for Windows and for Linux, and I had the same problem. Could anyone help me with that? I have analysed data from 454, but this is my first time with Ion Torrent data.

Thank you!

2

That’s a weird bug. Are you sure that it was downloaded/decompressed properly? I worry that it might have gotten corrupted in the file transfer.

Pat

3

Thank you pat!

I contacted the sequencing company and they told me the file was incomplete! THey will send me the correct file, then I will restart the analysis!
Thanks!
Marcelo

4

phew - glad to hear it worked out.

pat