Other than using sff.multiple, I follow the general work flow suggested in the 454 SOP.
What is the best way to both remove contaminating (human) sequences and then split my files into separate sff files for submission to SRA? I’ve got 3 original sff files with 44 samples, 16 done on more than one plate. Can the resulting fasta/groups/names files created after remove.lineage be used in some way?
What is the best way to both remove contaminating (human) sequences
Probably remove.lineage where you remove those sequences that classify as Eukarya.
split my files into separate sff files for submission to SRA?
try sff.info where you give it an oligos file
try sff.info where you give it an oligos file
How does that work when I have 3 different oligos files?
If you only have one sff file? Can you pool the oligos files?
I’ve got 3 original sff files with 44 samples, 16 done on more than one plate.
You should be able to run it three times with one oligo file per sff file
But then where do I do remove.lineage and get back to having sff files?
I understand how to do each command individually, and the resulting files. I just don’t get how to do BOTH and have files in a format acceptable to be submitted to a publicly accessible database.
I see, you want a new sff file without any human reads. Not sure we can do that. Are people really claiming that a human 18S sequence is PHI? That is a huge stretch since all humans have the same sequence, afik.