I am using the dada2 pipeline for analysis of paired-end sequecing data. I tried the tutorial and everything worked fine. For my analysis I need another database, because I am working with pmoA as functional marker. A research group published their database, but they used mothur and BLAST. However, there are files in fasta format and I tried them. assignTaxonomy() does not work. Following error appears:
Fehler in .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec, :
reading FASTA file C:/Users/user/Desktop/Uni/Master MolMi/Forschungsmodul/Tanja Testsequenzen/pmoA/pmoa.mothur.2013.test2.fasta: cannot read line 1, line is too long
I checked the format used for the reference data in assignTaxonomy(), but did not find any fault.
Do you have any idea?