I’m using sffinfo within mothur as follows:
mothur -q “#sffinfo(sff=454Reads.RL6.sff, flow=F);”
I get the FASTA & QUAL files as expected. What I’ve noticed is that an extra base ( one more than what is indicated in “Clip Qual Right:” ) is trimmed off. Looks like it may be an off-by-one bug here. A visual look at the soft masked bases within the SFF file can confirm this as well.
With regards to “Clip Qual Right:” , this is not how sffinfo from 454tools or process_sff.py from QIIME is functioning during SFF to FASTA conversion.
Can you confirm this behavior on your end? Am I missing something obvious? I will admit I’m a new user to mothur and how SFF files are processed.
Let me know if you require me to provide some examples.
Thanks for your support on this.