# HG changeset patch # User simon-gladman # Date 1542080534 18000 # Node ID 9fbb104e16d92a5fe41b1240a0d800884cca4bd9 # Parent 910739de7b8088a64eeb7dea6fe922d343bd91ba update diff -r 910739de7b80 -r 9fbb104e16d9 phyloseq_filter.R --- a/phyloseq_filter.R Wed Sep 05 22:21:43 2018 -0400 +++ b/phyloseq_filter.R Mon Nov 12 22:42:14 2018 -0500 @@ -2,10 +2,10 @@ library('ape') library('ggplot2') suppressPackageStartupMessages(library('phyloseq')) -library(biomformat) library(plyr) Sys.setenv("DISPLAY"=":1") library(biomformat) +library(jsonlite) suppressPackageStartupMessages(library(metagenomeSeq)) suppressPackageStartupMessages(library("doParallel")) ncores = ceiling(detectCores() * 0.8) @@ -65,6 +65,12 @@ pngfile_post_phyla_filtering<- gsub("[ ]+", "", paste(options$outdir,"/barplot_after_phyla_filtering.png")) htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) +### overwrite the write_biom function for proper BIOM format +### https://github.com/smdabdoub/biomformat/blob/master/R/IO-methods.R#L124 +write_biom <- function(x, biom_file){ + cat(toJSON(x, always_decimal=TRUE, auto_unbox=TRUE), file=biom_file) +} + ### This function accepts different two different type of BIOM file format readBIOM<-function(inBiom){ tryCatch({ @@ -152,7 +158,7 @@ #png('barplot_pre_phyla_filtering.png') bitmap(pngfile_pre_phyla_filtering,"png16m") - print(sample_data(physeq_pre_phyla_filtering)) + #print(sample_data(physeq_pre_phyla_filtering)) barplot_pre_phyla_filtering<-plot_bar(physeq_pre_phyla_filtering, x=colnames(sample_data(physeq_pre_phyla_filtering))[1], fill=kingdom_str) + geom_bar(stat="identity", position="stack") + labs(title=paste("Sample Depth Bar Chart",kingdom_str,sep=":"),subtitle="Sample Vs Abundance (Pre Phyla Filtering)",caption="source: Input Biom") + @@ -181,7 +187,7 @@ create_HTML<-function(htmlfile){ htmlfile_handle <- file(htmlfile) html_output = c('', - '', '', '', '', '

', '

', @@ -203,7 +209,7 @@ '

', - ''); + ''); writeLines(html_output, htmlfile_handle); close(htmlfile_handle); } @@ -212,7 +218,7 @@ temp.df<-data.frame(otu_table(physeq_obj)) temp.df.counts<-as.data.frame(colSums(temp.df)) colnames(temp.df.counts)<-"Abundance" - print(temp.df.counts) + #print(temp.df.counts) return(temp.df.counts) } @@ -317,12 +323,19 @@ physeq_filter_post_transform = prune_taxa((tax_table(physeq_filter_post_transform)[, kingdom_str] %in% topphyla_post_transform), physeq_filter_post_transform) + ### remove samples with zero value + otu_table(physeq_filter_post_transform)<-otu_table(physeq_filter_post_transform)[,colSums(otu_table(physeq_filter_post_transform)) > 0] create_PDF(pdffile,before_filtering_dataframe_sampleCounts,after_filtering_dataframe_sampleCounts,physeq_filter_pre_transform,physeq_filter_post_transform,kingdom_str,htmlfile,pngfile_before_filtering,pngfile_after_filtering,pngfile_pre_phyla_filtering,pngfile_post_phyla_filtering) ### convert phyloseq object to metagenomeSeq - preparing for BIOM output - metagenomeSeq_obj <- phyloseq_to_metagenomeSeq(physeq_filter_post_transform) - metagenomeSeq_biom <- MRexperiment2biom(metagenomeSeq_obj) + #metagenomeSeq_obj <- phyloseq_to_metagenomeSeq(physeq_filter_post_transform) + #metagenomeSeq_biom <- MRexperiment2biom(metagenomeSeq_obj) + + biom_obj=make_biom(otu_table(physeq_filter_post_transform),sample_metadata=sample_data(physeq_filter_post_transform),observation_metadata=tax_table(physeq_filter_post_transform),matrix_element_type="float") + biom_obj_2_metagenomeSeq_obj<-biom2MRexperiment(biom_obj) + metagenomeSeq_biom <- MRexperiment2biom(biom_obj_2_metagenomeSeq_obj) + ## write biom file write_biom(metagenomeSeq_biom, biom_file=options$outbiom) diff -r 910739de7b80 -r 9fbb104e16d9 phyloseq_filter.xml --- a/phyloseq_filter.xml Wed Sep 05 22:21:43 2018 -0400 +++ b/phyloseq_filter.xml Mon Nov 12 22:42:14 2018 -0500 @@ -70,11 +70,11 @@ - - + + @@ -94,22 +94,20 @@ **What it does** -Filter BIOM file using R package called phyloseq_. +Filter out low abundance OTUs and/or data corresponding to the least represented taxonomic grouping using R package called R_package_called_phyloseq_, and specifically according to the pre-processing step outlined in the Phyloseq_Ordination_Plot_Tutorial_. -.. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html +.. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html +.. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html ----- **Input** -- **Choose an input file type** - BIOM File or TABULAR file -- **OTU TABLE** - this is a OTU matrix -- **Taxonomy TABLE** - this is a TAX matrix -- **Metadata TABLE** - this is a metadata file of the experiment design -- **Select a taxonomic rank for the analysis** - select a taxonomy for filtering -- **Specify value of Y (where 1.0=100%)** - Filter out OTUs from the analysis that do not appear more than X times in more than Y% of the samples -- **Specify value of X** - Remove OTUs that do not appear more than X times (e.g., 5 times) -- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - taxonomic rank units (e.g. Phyla, Class etc) to keep +- **Choose an input file type** - either 1 BIOM file or 3 TABULAR files (i.e. OTU, Taxonomy and Metadata tables) +- **Select a taxonomic rank for the analysis** - if filtering out low abundance taxa, this is the level of the taxonomy that you want to filter on (e.g. phyla, species) +- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - the number of the most abundant taxonomic rank units specified above to keep (e.g. remove all the most abundant 5 phyla or species) +- **Specify value of X** - if filtering out low abundance OTUs, use this to specify a value of X (where OTUs are removed that do not appear more than X times in more than Y% of the samples) +- **Specify value of Y (where 1.0=100%)** - if filtering out low abundance OTUs use this to specify a value of Y (where OTUs are removed that do not appear more than X times in more than Y% of the samples) ----- diff -r 910739de7b80 -r 9fbb104e16d9 test-data/barplot_after_filtering.png Binary file test-data/barplot_after_filtering.png has changed diff -r 910739de7b80 -r 9fbb104e16d9 test-data/barplot_after_phyla_filtering.png Binary file test-data/barplot_after_phyla_filtering.png has changed diff -r 910739de7b80 -r 9fbb104e16d9 test-data/barplot_before_filtering.png Binary file test-data/barplot_before_filtering.png has changed diff -r 910739de7b80 -r 9fbb104e16d9 test-data/barplot_before_phyla_filtering.png Binary file test-data/barplot_before_phyla_filtering.png has changed diff -r 910739de7b80 -r 9fbb104e16d9 test-data/biom_out.biom --- a/test-data/biom_out.biom Wed Sep 05 22:21:43 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"id":{},"format":["Biological Observation Matrix 1.0.0-dev"],"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],"type":["OTU table"],"generated_by":["metagenomeSeq 1.20.0"],"date":["2018-09-05 13:01:33"],"matrix_type":["dense"],"matrix_element_type":["int"],"shape":[204,26],"rows":[{"id":["12812"],"metadata":{"taxonomy":["12812","Bacteria","Actinobacteria","Actinobacteria","koll13"]}},{"id":["546222"],"metadata":{"taxonomy":["546222","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":["313857"],"metadata":{"taxonomy":["313857","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["252398"],"metadata":{"taxonomy":["252398","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["331093"],"metadata":{"taxonomy":["331093","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["317658"],"metadata":{"taxonomy":["317658","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["329744"],"metadata":{"taxonomy":["329744","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["242450"],"metadata":{"taxonomy":["242450","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":["556066"],"metadata":{"taxonomy":["556066","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Microbacteriaceae","Agromyces"]}},{"id":["543491"],"metadata":{"taxonomy":["543491","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia"]}},{"id":["58301"],"metadata":{"taxonomy":["58301","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiaaeria"]}},{"id":["471141"],"metadata":{"taxonomy":["471141","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiamucilaginosa"]}},{"id":["13034"],"metadata":{"taxonomy":["13034","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Mycobacteriaceae","Mycobacterium"]}},{"id":["469868"],"metadata":{"taxonomy":["469868","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumdentium"]}},{"id":["326977"],"metadata":{"taxonomy":["326977","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumadolescentis"]}},{"id":["469873"],"metadata":{"taxonomy":["469873","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumpseudocatenulatum"]}},{"id":["471180"],"metadata":{"taxonomy":["471180","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium"]}},{"id":["60254"],"metadata":{"taxonomy":["60254","Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":["589787"],"metadata":{"taxonomy":["589787","Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":["535929"],"metadata":{"taxonomy":["535929","Bacteria","Cyanobacteria","Chloroplast","Cryptophyta"]}},{"id":["308887"],"metadata":{"taxonomy":["308887","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["278521"],"metadata":{"taxonomy":["278521","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["561077"],"metadata":{"taxonomy":["561077","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["542011"],"metadata":{"taxonomy":["542011","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["332808"],"metadata":{"taxonomy":["332808","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["317182"],"metadata":{"taxonomy":["317182","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["549656"],"metadata":{"taxonomy":["549656","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["327536"],"metadata":{"taxonomy":["327536","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["340216"],"metadata":{"taxonomy":["340216","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["279599"],"metadata":{"taxonomy":["279599","Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae","Dolichospermum"]}},{"id":["235567"],"metadata":{"taxonomy":["235567","Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae"]}},{"id":["557211"],"metadata":{"taxonomy":["557211","Bacteria","Cyanobacteria","Synechococcophycideae","Synechococcales","Synechococcaceae","Prochlorococcus"]}},{"id":["263681"],"metadata":{"taxonomy":["263681","Bacteria","Cyanobacteria","4C0d-2","YS2"]}},{"id":["162077"],"metadata":{"taxonomy":["162077","Bacteria","Proteobacteria","Epsilonproteobacteria","Campylobacterales","Campylobacteraceae","Campylobacter","Campylobacterconcisus"]}},{"id":["361480"],"metadata":{"taxonomy":["361480","Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Alcaligenaceae"]}},{"id":["228077"],"metadata":{"taxonomy":["228077","Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":["540352"],"metadata":{"taxonomy":["540352","Bacteria","Proteobacteria","Betaproteobacteria","Neisseriales","Neisseriaceae"]}},{"id":["360229"],"metadata":{"taxonomy":["360229","Bacteria","Proteobacteria","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South Carolina Pine soil, pH 4.9"}},{"id":"CC1","metadata":{"X.SampleID":"CC1","Primer":"ILBC_02","Final_Barcode":"AACTCG","Barcode_truncated_plus_T":"CGAGTT","Barcode_full_length":"CATCGACGAGT","SampleType":"Soil","Description":"Cedar Creek Minnesota, grassland, pH 6.1"}},{"id":"SV1","metadata":{"X.SampleID":"SV1","Primer":"ILBC_03","Final_Barcode":"AACTGT","Barcode_truncated_plus_T":"ACAGTT","Barcode_full_length":"GTACGCACAGT","SampleType":"Soil","Description":"Sevilleta new Mexico, desert scrub, pH 8.3"}},{"id":"M31Fcsw","metadata":{"X.SampleID":"M31Fcsw","Primer":"ILBC_04","Final_Barcode":"AAGAGA","Barcode_truncated_plus_T":"TCTCTT","Barcode_full_length":"TCGACATCTCT","SampleType":"Feces","Description":"M3, Day 1, fecal swab, whole body study"}},{"id":"M11Fcsw","metadata":{"X.SampleID":"M11Fcsw","Primer":"ILBC_05","Final_Barcode":"AAGCTG","Barcode_truncated_plus_T":"CAGCTT","Barcode_full_length":"CGACTGCAGCT","SampleType":"Feces","Description":"M1, Day 1, fecal swab, whole body study "}},{"id":"M31Plmr","metadata":{"X.SampleID":"M31Plmr","Primer":"ILBC_07","Final_Barcode":"AATCGT","Barcode_truncated_plus_T":"ACGATT","Barcode_full_length":"CGAGTCACGAT","SampleType":"Skin","Description":"M3, Day 1, right palm, whole body study"}},{"id":"M11Plmr","metadata":{"X.SampleID":"M11Plmr","Primer":"ILBC_08","Final_Barcode":"ACACAC","Barcode_truncated_plus_T":"GTGTGT","Barcode_full_length":"GCCATAGTGTG","SampleType":"Skin","Description":"M1, Day 1, right palm, whole body study "}},{"id":"F21Plmr","metadata":{"X.SampleID":"F21Plmr","Primer":"ILBC_09","Final_Barcode":"ACACAT","Barcode_truncated_plus_T":"ATGTGT","Barcode_full_length":"GTAGACATGTG","SampleType":"Skin","Description":"F1, Day 1, right palm, whole body study "}},{"id":"M31Tong","metadata":{"X.SampleID":"M31Tong","Primer":"ILBC_10","Final_Barcode":"ACACGA","Barcode_truncated_plus_T":"TCGTGT","Barcode_full_length":"TGTGGCTCGTG","SampleType":"Tongue","Description":"M3, Day 1, tongue, whole body study "}},{"id":"M11Tong","metadata":{"X.SampleID":"M11Tong","Primer":"ILBC_11","Final_Barcode":"ACACGG","Barcode_truncated_plus_T":"CCGTGT","Barcode_full_length":"TAGACACCGTG","SampleType":"Tongue","Description":"M1, Day 1, tongue, whole body study "}},{"id":"LMEpi24M","metadata":{"X.SampleID":"LMEpi24M","Primer":"ILBC_13","Final_Barcode":"ACACTG","Barcode_truncated_plus_T":"CAGTGT","Barcode_full_length":"CATGAACAGTG","SampleType":"Freshwater","Description":"Lake Mendota Minnesota, 24 meter epilimnion "}},{"id":"SLEpi20M","metadata":{"X.SampleID":"SLEpi20M","Primer":"ILBC_15","Final_Barcode":"ACAGAG","Barcode_truncated_plus_T":"CTCTGT","Barcode_full_length":"AGCCGACTCTG","SampleType":"Freshwater","Description":"Sparkling Lake Wisconsin, 20 meter eplimnion"}},{"id":"AQC1cm","metadata":{"X.SampleID":"AQC1cm","Primer":"ILBC_16","Final_Barcode":"ACAGCA","Barcode_truncated_plus_T":"TGCTGT","Barcode_full_length":"GACCACTGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 0-1cm depth"}},{"id":"AQC4cm","metadata":{"X.SampleID":"AQC4cm","Primer":"ILBC_17","Final_Barcode":"ACAGCT","Barcode_truncated_plus_T":"AGCTGT","Barcode_full_length":"CAAGCTAGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 3-4 cm depth"}},{"id":"AQC7cm","metadata":{"X.SampleID":"AQC7cm","Primer":"ILBC_18","Final_Barcode":"ACAGTG","Barcode_truncated_plus_T":"CACTGT","Barcode_full_length":"ATGAAGCACTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 6-7 cm depth"}},{"id":"NP2","metadata":{"X.SampleID":"NP2","Primer":"ILBC_19","Final_Barcode":"ACAGTT","Barcode_truncated_plus_T":"AACTGT","Barcode_full_length":"TCGCGCAACTG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 1"}},{"id":"NP3","metadata":{"X.SampleID":"NP3","Primer":"ILBC_20","Final_Barcode":"ACATCA","Barcode_truncated_plus_T":"TGATGT","Barcode_full_length":"GCTAAGTGATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 2"}},{"id":"NP5","metadata":{"X.SampleID":"NP5","Primer":"ILBC_21","Final_Barcode":"ACATGA","Barcode_truncated_plus_T":"TCATGT","Barcode_full_length":"GAACGATCATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 3"}},{"id":"TRRsed1","metadata":{"X.SampleID":"TRRsed1","Primer":"ILBC_22","Final_Barcode":"ACATGT","Barcode_truncated_plus_T":"ACATGT","Barcode_full_length":"CACGTGACATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 1"}},{"id":"TRRsed2","metadata":{"X.SampleID":"TRRsed2","Primer":"ILBC_23","Final_Barcode":"ACATTC","Barcode_truncated_plus_T":"GAATGT","Barcode_full_length":"TGCGCTGAATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 2"}},{"id":"TRRsed3","metadata":{"X.SampleID":"TRRsed3","Primer":"ILBC_24","Final_Barcode":"ACCACA","Barcode_truncated_plus_T":"TGTGGT","Barcode_full_length":"GATGTATGTGG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 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South Carolina Pine soil, pH 4.9"}},{"id":"CC1","metadata":{"X.SampleID":"CC1","Primer":"ILBC_02","Final_Barcode":"AACTCG","Barcode_truncated_plus_T":"CGAGTT","Barcode_full_length":"CATCGACGAGT","SampleType":"Soil","Description":"Cedar Creek Minnesota, grassland, pH 6.1"}},{"id":"SV1","metadata":{"X.SampleID":"SV1","Primer":"ILBC_03","Final_Barcode":"AACTGT","Barcode_truncated_plus_T":"ACAGTT","Barcode_full_length":"GTACGCACAGT","SampleType":"Soil","Description":"Sevilleta new Mexico, desert scrub, pH 8.3"}},{"id":"M31Fcsw","metadata":{"X.SampleID":"M31Fcsw","Primer":"ILBC_04","Final_Barcode":"AAGAGA","Barcode_truncated_plus_T":"TCTCTT","Barcode_full_length":"TCGACATCTCT","SampleType":"Feces","Description":"M3, Day 1, fecal swab, whole body study"}},{"id":"M11Fcsw","metadata":{"X.SampleID":"M11Fcsw","Primer":"ILBC_05","Final_Barcode":"AAGCTG","Barcode_truncated_plus_T":"CAGCTT","Barcode_full_length":"CGACTGCAGCT","SampleType":"Feces","Description":"M1, Day 1, fecal swab, whole body study "}},{"id":"M31Plmr","metadata":{"X.SampleID":"M31Plmr","Primer":"ILBC_07","Final_Barcode":"AATCGT","Barcode_truncated_plus_T":"ACGATT","Barcode_full_length":"CGAGTCACGAT","SampleType":"Skin","Description":"M3, Day 1, right palm, whole body study"}},{"id":"M11Plmr","metadata":{"X.SampleID":"M11Plmr","Primer":"ILBC_08","Final_Barcode":"ACACAC","Barcode_truncated_plus_T":"GTGTGT","Barcode_full_length":"GCCATAGTGTG","SampleType":"Skin","Description":"M1, Day 1, right palm, whole body study "}},{"id":"F21Plmr","metadata":{"X.SampleID":"F21Plmr","Primer":"ILBC_09","Final_Barcode":"ACACAT","Barcode_truncated_plus_T":"ATGTGT","Barcode_full_length":"GTAGACATGTG","SampleType":"Skin","Description":"F1, Day 1, right palm, whole body study "}},{"id":"M31Tong","metadata":{"X.SampleID":"M31Tong","Primer":"ILBC_10","Final_Barcode":"ACACGA","Barcode_truncated_plus_T":"TCGTGT","Barcode_full_length":"TGTGGCTCGTG","SampleType":"Tongue","Description":"M3, Day 1, tongue, whole body study "}},{"id":"M11Tong","metadata":{"X.SampleID":"M11Tong","Primer":"ILBC_11","Final_Barcode":"ACACGG","Barcode_truncated_plus_T":"CCGTGT","Barcode_full_length":"TAGACACCGTG","SampleType":"Tongue","Description":"M1, Day 1, tongue, whole body study "}},{"id":"LMEpi24M","metadata":{"X.SampleID":"LMEpi24M","Primer":"ILBC_13","Final_Barcode":"ACACTG","Barcode_truncated_plus_T":"CAGTGT","Barcode_full_length":"CATGAACAGTG","SampleType":"Freshwater","Description":"Lake Mendota Minnesota, 24 meter epilimnion "}},{"id":"SLEpi20M","metadata":{"X.SampleID":"SLEpi20M","Primer":"ILBC_15","Final_Barcode":"ACAGAG","Barcode_truncated_plus_T":"CTCTGT","Barcode_full_length":"AGCCGACTCTG","SampleType":"Freshwater","Description":"Sparkling Lake Wisconsin, 20 meter eplimnion"}},{"id":"AQC1cm","metadata":{"X.SampleID":"AQC1cm","Primer":"ILBC_16","Final_Barcode":"ACAGCA","Barcode_truncated_plus_T":"TGCTGT","Barcode_full_length":"GACCACTGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 0-1cm depth"}},{"id":"AQC4cm","metadata":{"X.SampleID":"AQC4cm","Primer":"ILBC_17","Final_Barcode":"ACAGCT","Barcode_truncated_plus_T":"AGCTGT","Barcode_full_length":"CAAGCTAGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 3-4 cm depth"}},{"id":"AQC7cm","metadata":{"X.SampleID":"AQC7cm","Primer":"ILBC_18","Final_Barcode":"ACAGTG","Barcode_truncated_plus_T":"CACTGT","Barcode_full_length":"ATGAAGCACTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 6-7 cm depth"}},{"id":"NP2","metadata":{"X.SampleID":"NP2","Primer":"ILBC_19","Final_Barcode":"ACAGTT","Barcode_truncated_plus_T":"AACTGT","Barcode_full_length":"TCGCGCAACTG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 1"}},{"id":"NP3","metadata":{"X.SampleID":"NP3","Primer":"ILBC_20","Final_Barcode":"ACATCA","Barcode_truncated_plus_T":"TGATGT","Barcode_full_length":"GCTAAGTGATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 2"}},{"id":"NP5","metadata":{"X.SampleID":"NP5","Primer":"ILBC_21","Final_Barcode":"ACATGA","Barcode_truncated_plus_T":"TCATGT","Barcode_full_length":"GAACGATCATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 3"}},{"id":"TRRsed1","metadata":{"X.SampleID":"TRRsed1","Primer":"ILBC_22","Final_Barcode":"ACATGT","Barcode_truncated_plus_T":"ACATGT","Barcode_full_length":"CACGTGACATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 1"}},{"id":"TRRsed2","metadata":{"X.SampleID":"TRRsed2","Primer":"ILBC_23","Final_Barcode":"ACATTC","Barcode_truncated_plus_T":"GAATGT","Barcode_full_length":"TGCGCTGAATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 2"}},{"id":"TRRsed3","metadata":{"X.SampleID":"TRRsed3","Primer":"ILBC_24","Final_Barcode":"ACCACA","Barcode_truncated_plus_T":"TGTGGT","Barcode_full_length":"GATGTATGTGG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 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