Use of Kraken output for functional analysis
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11 weeks ago
Srinka ▴ 20

Is there anyone available to assist me in utilizing Kraken output for functional analysis? I've been on the lookout for tools capable of processing Kraken report output for functional analysis.

metagenomics kraken shotgun • 636 views
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You're going to have to be more specific. "Functional analysis" is a catchall for a lot of different types of possible downstream analyses. Finding recent studies that have similar data is a good place to start in finding appropriate tools.

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Hi, by functional analysis I meant the pathways the microbes are involved in.

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Hello,

You can convert your classified Kraken report to the BIOM format, and then use the PICRUSt tool to predict the functions associated with KEGG and COG based on the OTU information present in the samples.

Thanks!

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Hello, Thanks for your suggestion. I will surely try this.

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Can you please suggest any tool to help convert the Kraken report to BIOM format?

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Hello,

you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport

cheers,

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Hi,

I've gone over the tutorial section of the Picrust GitHub and am confused about the study_seqs.fna file.

  • What should you use for the study_seqs.fna file, and are there any edits required to it?

Context: I ask this because Picrust requires the sequence IDs in the fna file to be linked to the first column of the OTU table. My OTU table is taxa x sample (row x col) and can be linked back to the kraken database I used. I am worried about the IDs in the database. After looking through the database fasta file, I found that multiple sequences linked to the same kraken id (taxa). My first assumption is to combine these sequences into one under the one ID, but I am worried this would negatively impact the alignment process in picrust. However, if I only choose one sequence then is there a way to decide which sequence is the best? If the fna file is supposed to be the ASVs linked to the specific sample, then I have no clue where to start to link those reads to the OTU table.

Many thanks.

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