I have 20 .sff files (IonTorrent) that I want to merge using the merge.sfffiles command.
I want to merge the files to ensure maximum power for the denoising procedure.
Each .sff file corresponds to a specific bar-coded sample, and has an unique key.
When I want to merge the .sff files I get a warning that the key sequences do not match.
Using the keytrim option this problem can be solved. I wonder if I will be able to seperate on barcode
later when using this feature?
There is however another problem.
Mothur throws an error saying the key length is not equal. This is correct: 16 key sequences have a length of 17
while 4 other key sequences are of length 18 or 19. As a result Mothur does not merge the files.
Is there any way to deal with this error?
Any help is greatly appreciated.
So I figured out I can merge the IonTorrent SFF files using the sfffile program which is part of the gsSeqTools package provided by Roche 454 (can be downloaded/requested here: http://454.com/contact-us\software-request.asp).
Now a new question arises
For the denoising procedure (shhh.flows) I need a LookUp file for the IonTorrent platform.
Files are provided for the 454 platform, but not for IonTorrent.
I understand I can generate a LookUp file using the seq.error and make.lookup commands.
Unfortunately I did not sequence mock community samples of known composition.
Are there any LookUp files available for IonTorrent?
I welcome any advise/suggestions.
Way back when I made a script to generate a lookup file for IonTorrent data. I didn’t push it because the sequence data were so bad that I didn’t want to publish a paper bashing the method - I even got IT to generate the data for us. It wound up not really mattering what I used for the LookUp file and even with it, I wasn’t able to get a good handle on what the minflows/maxflows value should have been. I’d suggest using the qscore appraoch we outline for 454 data.