How to have species taxonomy appear with Taxonomy ids; Greengenes reference db

Question

[travisreid99]

I have about 100,000 sequences and I am using blast with greengenes (the lastest version) as a reference database. Whenever I run it, I get an outcome like

Query= SWED-1-1_0 HISEQ:265:HHK2LBCXX:1:1101:3356:2270 1:N:0:ACAGCAGA orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0 Length=429 Score E Sequences producing significant alignments: (Bits) Value 4469610 787 0.0
4451440 787 0.0
714887 787 0.0
887750 787 0.0

I would like to know how to attach have the actual taxonomy appear instead of the ids. For example it would say "4469610 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__." I have the greengenes taxonomy text file, I just need to know I to make it appear in the outcome. Apparently a way to do this is to add the info into the head of the fasta file such as ">idxxx taxonomy\nseq", but I have not gotten that to work nor have I found any other information on something like this. Any help is appreciated.

Answer 1

[natasha.sernova]

See this post:

how to map greengenes taxonomy locally

at the bottom see the answer for taxonomy

these articles also may help:

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280142/

assign_taxonomy.py – Assign taxonomy to each sequence

http://qiime.org/scripts/assign_taxonomy.html