search

swo / caravan

a 16S pipeline
0 stars 3 forks source link

dealing with forward and reverse barcodes #6

Closed elsherbini closed 8 years ago

elsherbini commented 8 years ago

in caravan/barcodes.py, it appears to only handle the case where you have a single barcode thats unique to a sample. I often have samples that are only identifiable by the unique combination of forward and reverse barcodes. The reverse barcode gets extracted and placed into the header, but the forward barcode is in the forward read itself.

Have you run into this before? Should I code up something to handle forward barcodes?

elsherbini commented 8 years ago

inline barcodes are already supported by making use of the truncate utility. For instance, with inline barcodes of length 8, you could:

van.py truncate length 8 | van.py demultiplex