metabarfactory/metabar_external_data

repository of data examples for the R package metabaR

metabaR external data

This folder is a repository of external resources and toy data examples for the R package metabaR:

SILVA Taxonomy

• release 138.1 : tax_slv_ssu_138.1.txt

Raw data tables for the soil_euk dataset

Basic table inputs

• litiere_euk_reads.txt:
  A PCR (rows) by OTU (columns) table: amount of reads of each OTU in each PCR.
• litiere_euk_motus.txt:
  A OTU (rows) by OTU information (columns) table: e.g. taxonomy, sequence, etc.
• litiere_euk_pcrs.txt:
  A PCR (rows) by PCR information (columns) table: e.g. PCR plate coordinates, primers used, etc.
• litiere_euk_samples.txt:
  A sample (rows) by sample information (columns) table: e.g. geographic coordinates.

Obitools inputs

• litiere_euk_cl97_agg_filt_tax.tab:
  A OTU/seq (rows) by OTU informations (columns; including # reads in a given sample, taxonomy, sequence, etc.). Typically an output from obitools (obitab).
• ngsfilter_GWM-768.new_2.txt:
  A PCR (rows) by PCR information (columns; any PCR related metadata). Typically a ngsfilter txt file.
• Litiere_sample_list_2.txt:
  A sample (rows) by sample information (columns; any metadata for samples)

BIOM input

• litiere_euk_reads_hdf5.biom:
  Soil_euk dataset in the BIOM format.

SILVAngs outputs

• lit_euk---ssu---otus.csv:
  A file containing taxonomic assignments for each sequence submitted to SILVAngs
• lit_euk---ssu---sequence_cluster_map---litiere_euk_cl97_agg_filt.clstr:
  A file containing the mapping of each sequence submitted to SILVAngs. Even if no clustering is supposed to be done (i.e. sequence similarity set at 100% in the pipeline), sequences that are strict suffix/prefix of another can still be clustered together with the clustering algorithm used by SILVAngs (CD-HIT).

The karst_euk dataset

• karst_euk.rds:
  A metabarlist corresponding to the karst_euk dataset. To be loaded using the readRDS function.

The h20_plants dataset

• h20_plants.rds:
  A metabarlist corresponding to the h20_plants dataset. To be loaded using the readRDS function.