-
Notifications
You must be signed in to change notification settings - Fork 0
/
Metadata and metabarcoding README
94 lines (88 loc) · 6.7 KB
/
Metadata and metabarcoding README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
Protecting Our River README
For help, contact Miroslava Munguia Ramos(mnmungui@ucla.edu) or Rachel Meyer (rameyer@ucsc.edu) or report an issue here in Github.
**** These datasets are not publication ready! Sequence data and clean datasets will be released as a citable dataset in June.
**** If you are interested in using these data or part of the data for classes or workshops, we ask that you contact Miroslava and Rachel and let them know so they grant permission.
**** We wish you great exploring the preliminary data and results from the Protecting Our River project!
This repository will grow as we add new data and analyses.
Current metabarcode markers used:
Vert12S \ Riaz et al., 2011 (https://doi.org/10.1093/nar/gkr732) \ F: TAGAACAGGCTCCTCTAG \ R: TTAGATACCCCACTATGC
18S \ Amaral-Zettler et al. 2009 and Stoek et al. 2010 (http://doi.org/10.1371/journal.pone.0006372)\ Euk1391F: GTACACACCGCCCGTC \ EukBR: TGATCCTTCTGCAGGTTCACCTAC
16S \ Parada and Appriil primers modified from Caporaso et al 2011 (http://doi.org/10.1111/1462-2920.13023) \ 515F (Parada): GTGYCAGCMGCCGCGGTAA \ 806R (Apprill): GACTACNVGGGTWTCTAAT
PITS \ Chen et al., 2010 (https://doi.org/10.1371/journal.pone.0008613) \ S2F: ATGCGATACTTGGTGTGAAT \ S3R: GACGCTTCTCCAGACTACAAT
FITS \ White et al., 1990; Epp et al., 2012 (https://doi.org/10.1111/j.1365-294X.2012.05537.x) \ ITS5 F: GGAAGTAAAAGTCGTAACAAGG \ 5.8S_R: CAAGAGATCCGTTGTTGAAAGTT
CO1 \ Leray et al., 2013; Folmer et al., 1994 (https://doi.org/10.1186/1742-9994-10-34) \ mlCOIintF: GWACWGGWTGAACWGTWTAYCCYCC \ jgHCO2198: TAIACYTCIGGRTGICCRAARAAYCA
Foundational files:
Metadata: POUR_Round1_2020_06_01_2020_09_15_WITHSTATS.csv
*Detailed.txt files that have the original ASVs along with the Bayesian confidence scores for each hierarchical level of taxonomic classification. We ran these separately for the first 96 samples and the second batch of ~59 samples so each marker has two corresponding files containing its ASVs. In time we will provide these, merged, probably when we run everything together from the entire three timepoints of the project.
POUR1_all_physeq_[MARKER]m.txt files are the taxonomy tables from ROUND 1 with columns as samples and row as taxa. Units are total DNA reads per taxon per sample.
Metadata explanation:
name
latitude
longitude
GPS_Precision
Bottom = concrete channel or soft bottom
LA River Site = sampling location name
Placed_Sample_Gen = whether tributary or main river
Placed_Sampled_Detailed = description of river section sampled whether pool/wash/river/creek/stream/reserve
Substrate = sediment or water (DB is drip bottle, PN is plankton net)
Site_Gen_Detailed = combination of LA River site, place sampled general, and detailed river characteristic (previous three variables)
alpha_PITS_observed = observed number of unique taxa for the metabarcode specified
alpha_FITS_observed = observed number of unique taxa for the metabarcode specified
alpha_16S_observed = observed number of unique taxa for the metabarcode specified
alpha_18S_observed = observed number of unique taxa for the metabarcode specified
alpha_CO1_observed = observed number of unique taxa for the metabarcode specified
alpha_Vert12S_observed = observed number of unique taxa for the metabarcode specified
bio01 = bioclim Annual Mean Temperature
bio02 = bioclim Mean Diurnal Range (Mean of monthly (max temp - min temp))
bio03 = bioclim Isothermality (BIO2/BIO7) (×100)
bio04 = bioclim Temperature Seasonality (standard deviation ×100)
bio05 = bioclim Max Temperature of Warmest Month
bio06 = bioclim Min Temperature of Coldest Month
bio07 = bioclim Temperature Annual Range (BIO5-BIO6)
bio08 = bioclim Mean Temperature of Wettest Quarter
bio09 = bioclim Mean Temperature of Driest Quarter
bio10 = bioclim Mean Temperature of Warmest Quarter
bio11 = bioclim Mean Temperature of Coldest Quarter
bio12 = bioclim Annual Precipitation
bio13 = bioclim Precipitation of Wettest Month
bio14 = bioclim Precipitation of Driest Month
bio15 = bioclim Precipitation Seasonality (Coefficient of Variation)
bio16 = bioclim Precipitation of Wettest Quarter
bio17 = bioclim Precipitation of Driest Quarter
bio18 = bioclim Precipitation of Warmest Quarter
bio19 = bioclim Precipitation of Coldest Quarter
grtgroup = USGS predicted soil great groups at 250 m
soil pH in H20 = OpenLandMap Soil pH in H2O
soil organic carbon = OpenLandMap Soil organic carbon content
soil sand = OpenLandMap Soil sand
soil clay = OpenLandMap Soil clay
elevation = USGS National Elevation Dataset 1/3 arc-second Elevation of sampling site
slope = USGS rate of change of elevation for each digital elevation model (DEM) cell
aspect = USGS direction of slope
NDVI Landsat 8 NDVI dataset Normalized Difference Vegetation Index in 32 days period
EVI Landsat 8 EVI dataset
greenness = Annual Greenest Pixel in the year of 2017
landcover = National Land Cover Database 2011 landcover code
impervious = Percent of the pixel covered by developed impervious surface
percent_tree_cover = Percent of the pixel that's covered by tree canopy
NBRT = Normalized Burn Ratio Thermal (NBRT) index in 32 days period
B1 = Sentinel-2 spectral band 1 (Wavelength: 443.9nm (S2A) / 442.3nm (S2B); Description: Aerosols)
B2 = Sentinel-2 spectral band 2 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Blue)
B3 = Sentinel-2 spectral band 3 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Green)
B4 = Sentinel-2 spectral band 4 (Wavelength: 664.5nm (S2A) / 665nm (S2B); Description: Red)
B5 = Sentinel-2 spectral band 5 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Vegetation red edge)
B6 = Sentinel-2 spectral band 6 (Wavelength: 740.2nm (S2A) / 739.1nm (S2B); Description: Vegetation red edge)
B7 = Sentinel-2 spectral band 7 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Vegetation red edge)
B8 = Sentinel-2 spectral band 8 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: NIR)
B8A = Sentinel-2 spectral band 8A (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Narrow NIR)
B9 Sentinel-2 spectral band 9 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: Water vapor)
B10 = Sentinel-2 spectral band 10 (Wavelength: 1373.5nm (S2A) / 1376.9nm (S2B); Description: SWIR Cirrus)
B11 = Sentinel-2 spectral band 11 (Wavelength: 1613.7nm (S2A) / 1610.4nm (S2B); Description: SWIR 1)
B12 = Sentinel-2 spectral band 12 (Wavelength: 945nm (S2A) / 943.2nm (S2B); Description: SWIR)
Plankton_tow_net_end_Latitude
Plankton_tow_net_end_Longitude
Plankton_tow_net_end_Precision
Habitat_description = details of how terrestrial or aquatic the sampling site is, best guess as to how frequently submerged the site is
Depth = depth below surface where sample was collected
Environmental_feature_type = CALeDNA category of environment
Image_file = name to connect the photograph taken in Kobo webform to sample