Getting representative sequences in fasta format

(Elizabeth S Bent) #1

Hi, I don’t normally use qiime, but a collaborator has given me a .biom file without metadata and a lot of raw fastq reads (not yet paired). I can convert the file to .txt format so I can use the data, but there is no sequence information in the file that I used (I used biom convert tool from Biom Project). What commands does she have to use to get a sequence file for the representative sequences she has generated in her analysis in fasta format so I can actually use it?

Thank you

(Matthew Ryan Dillon) #2

Has she tried exporting her FeatureData[Sequence] Artifact that was generated at the same time as the FeatureTable[Frequency]?

(Elizabeth S Bent) #3

I think she has managed to figure it out, so probably that is what she has done. Thank you, though.