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.
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written
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travisreid99 •
1 answer
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
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