The workflow
On 02/15/2013 01:08 PM, jjv5 wrote:
> Hello All,
>
> We're trying to get some taxonomic and functional profiles using ray
> meta. We find the xml output of profiles a bit confusing. We are used
> to generating standard abundance tables in biom format.
I did not know about the biom file format.
Can you open an issue and say that you would like biom file support at this
address:
https://github.com/sebhtml/ray/issues/new
This file contains proportions for genomes provided with -search
$ head Assembly/BiologicalAbundances/0.Profile.Bacteria-Genomes.tsv
#Name Proportion
Acidovorax_citrulli_AAC00_1_uid58429 0.00309393
Brevundimonas_subvibrioides_ATCC_15264_uid42117 0.000474785
Pusillimonas_T7_7_uid66391 0.000556296
Pseudomonas_entomophila_L48_uid58639 0.00543203
Bradyrhizobium_BTAi1_uid58505 0.00108658
Polaromonas_JS666_uid58207 0.00170638
Pseudomonas_putida_W619_uid58651 0.00437455
Ralstonia_solanacearum_GMI1000_uid57593 0.00162968
Methylobacterium_extorquens_AM1_uid57605 0.00977851
> I was
> wondering if any here is also in this same boat and could share a
> complete workflow.
>
> Does anyone use the output of ray meta as input to metarep for further
> analysis?
>
> Jim
>
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