Question: What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
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gravatar for tianshenbio
5 months ago by
tianshenbio70
tianshenbio70 wrote:

I have a newly constructed transcriptome blasted against NCBI nr database, Now I am using three tools to perform GO annotation, interproscan, blast2go, and eggnog. I wonder if there is a proper way to pool the results? I tried to merge the results in omicsbox (blast2go), I can see some terms that are too general were removed. Is there a better way to do that?

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by tianshenbio70
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It depends on what you mean by "pool the results". Would you like to produce a table that includes that annotation from each of these tools for each transcript? If so, you might want to try EnTAP, which is a new transcriptome annotation tool that wraps all of the tools you mentioned in your question (and many more). It reports the results in a .tsv 30 fields long and can automatically produce summary tables/graphics from the run as well. It also leverages Diamond, which can run many times faster than BLAST on large datasets like transcriptomes. Here's the docs page for EnTAP

ADD REPLYlink written 3 months ago by geneticatt30

I would also mention EnTAP. I started testing it massively and made some suggestions to the devs, which they quickly pushed to a newer version. EnTAP outputs Gene Ontology (via EggNOG) counts per transcript in figures format, but I can use the respective text format of the counts to plot beautifull publication-ready bar- and pie- plots with R. Another reason to use EnTAP is that you can easily build DIAMOND databases from any protein fasta. I am currenty using nr, refseq, swissprot, eggnog and some custom sets.

ADD REPLYlink written 18 days ago by Arsenal20
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