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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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RPK calculation #7

Closed nabilquraishi closed 6 years ago

nabilquraishi commented 6 years ago

Hi, Really like FMAP, starting to learn how to use it. Just wondered how you calculated RPK - I saw your code says readRpk = 1 / ($proteinLength * 3 / 1000). Wondered why you multiplied proteinlength by 3. Shouldnt it just be readRpk = 1 / ($proteinLength / 1000)?

Also would there be a update that builds a database on the entire Uniref90 for mapping and quantification rather than just the IDs that have KO. I would like to use it for gene enrichment analysis using GO.

Thanks, Nabil

jiwoongbio commented 6 years ago

Hi Nabil,

The sequencing reads are nucleotide-level and the mapping database is protein-level. To resolve the discordance between nucleotide-level and protein-level, we multiply 3 on the protein length and obtain the CDS length of nucleotide-level.

I am sorry to let you know that we have never planned to add a new function of UniRef database only because one key feature of FMAP is providing a protein database including orthology information.

Thanks, Jiwoong

On Sat, Feb 10, 2018 at 7:31 AM, nabilquraishi notifications@github.com wrote:

Hi, Really like FMAP, starting to learn how to use it. Just wondered how you calculated RPK - I saw your code says readRpk = 1 / ($proteinLength * 3 / 1000). Wondered why you multiplied proteinlength by 3. Shouldnt it just be readRpk = 1 / ($proteinLength / 1000)?

Also would there be a update that builds a database on the entire Uniref90 for mapping and quantification rather than just the IDs that have KO. I would like to use it for gene enrichment analysis using GO.

Thanks, Nabil

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nabilquraishi commented 6 years ago

Ah of course that makes sense! Thanks Jiwoong.