See also
OTU / denoising
pipeline
Read preparation
Sometimes machine-specific sequences appear in the reads. For example, 454
reads often start with the control sequence TCAG which is used for
calibrarion, though the four letters may come in a different order, and they
may have been stripped before you get the reads. If the sequence has a fixed
length and appears at the start of the read, it can be stripped by the
fastx_truncate command using the same
strategy used to strip primer sequences.
If you're not sure exactly what is in your reads, machine-specific sequences
are often noticable when you align OTUs to a
reference database.