Hi Patrick and sarah
First, thanks for developping MOTHUR, it is a GREAT software. However, it would be totally killer if MOTHUR could reassemble the shared file with the list, the taxonomy and the fasta file to provide one table of abundance per cut-off value in which each column is a group and each line an OTU, and also add the sequence identifier, its sequence and its taxonomy using the rdp classifier algorithm. Basically I would like to obtain a file lookin like the following:
Costello.Label.0.1.rawcounts.csv
F11Fcsw F12Fcsw F13Fcsw F14Fcsw Seqname Sequence Taxonomy
200 0 0 235 Seq234_GTUYU AA…TTA Bacteria;Firmicutes;Unclassified
450 0 0 4565 Seq4534_GSDEU AT…TCA Bacteria;Proteobacteria;Unclassified
56 0 0 8235 Seq245_GTJUU TT…TTG Bacteria;Firmicutes;Unclassified
Ideally MOTHUR would generate 2 files per cutoff level available in the shared file, one being the raw counts and the other being the relative abundances. I did write a little matlab script doing the step described above, and also compiled it as a .exe. I can send both of these if you wish but they are quite poorly written. I actually use loops to extract the interesting lines from the .shared file and extract the name of a sequence representative for each OTU from the list file. Based on that I can link each OTU to a sequence (using the .fasta file) and a taxonomy (.taxonomy file), and paste everything automatically in a xls file. It would be SOOOOOOOOO much easier to do everything in MOTHUR, especially because I don’t have access to Matlab anymore. (and it would be a lot neater)
Looking forward to hearing from you,
regards
Olivier Zemb