16s analysis for one sample

[litali]

How can I perform an analysis for one sample 454 16s sequences?
I thought to use qiime, but there are steps relating to the barcodes. I don't have barcodes in my sequences, only primers.

[rhinoceros]

You don't need barcodes for QIIME. QIIME's documentation is IMO rather poor but you can read about non-barcoded input e.g. here.

[Ciaran]

Qiime, is a series of scripts that forms a pipeline.
Just start the pipeline from the step post demultiplexing.

qiime

[litali]

qiime for one sample

but if I skip the demultiplexing step how will the linkerprimer be removed? I understand that it is the demultiplexing step that usually performs it..

[rhinoceros]

but if I skip the demultiplexing step how will the linkerprimer be removed? I understand that it is the demultiplexing step that usually performs it..

But why would you skip it? If your libraries don't have barcodes then you simply specify this for split_libraries.py with -b 0 (=barcode length is zero)

[litali]

qiime for one sample

But why would you skip it? If your libraries don't have barcodes then you simply specify this for split_libraries.py with -b 0 (=barcode length is zero)

In previous response Ciaran suggested that I should start the pipeline from the step post demultiplexing, tha's why I asked that if I start post demultiplexing, I actually start with the Pick otus step , so the primers are left. My library is only one sample and the reads begin from the primer (without the adaptor) so maybe it is ok?