illumina hiseq data, enviromental sample, how to look for some functional genes, os: ubuntu

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8.9 years ago

li.4001 • 0

New to this area, I'm trying to look for some functional genes from environmental microbiome sample. Illumina hiseq data generated, and I'm trying to blast the data with my functional gene database, any recommended tools? Or where to start with?

Operating system is Ubuntu 12.04

In addition, is there any recommended tools for assembly, annotation, and abundance analysis?

Thanks a lot!

gene next-gen Assembly blast sequence • 1.5k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 8.9 years ago by li.4001 • 0

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The important information to give is what kind of data? Rna-Seq or DNA-Seq? What is your functional gene database contains?

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 8.9 years ago by GouthamAtla 12k

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It's DNA-seq.

The database is an antibiotic resistant genes nucleotide database, contains 7279 genes.

ADD REPLY • link 8.9 years ago by li.4001 • 0

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