From 949f28fbe09d8863ba59d43c109744f78220ba95 Mon Sep 17 00:00:00 2001 From: Michael McLaren Date: Fri, 28 Feb 2020 09:26:22 -0500 Subject: [PATCH] Add table of just ASVs explicitly mentioned in manuscript --- analysis/export-asv-information.Rmd | 14 ++++++++++++-- results/manuscript-asv-sequences-and-taxonomy.csv | 13 +++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 results/manuscript-asv-sequences-and-taxonomy.csv diff --git a/analysis/export-asv-information.Rmd b/analysis/export-asv-information.Rmd index e473ae5..555d07a 100644 --- a/analysis/export-asv-information.Rmd +++ b/analysis/export-asv-information.Rmd @@ -30,8 +30,18 @@ figure3_asvs <- c("ASV4", "ASV10", "ASV20", "ASV37", "ASV62", "ASV82", tb0 <- tb %>% filter( genus == "Clostridioides" | - ncbi_species == "[Clostridium] hiranonis" | - feature_id %in% figure3_asvs + ncbi_species == "[Clostridium] hiranonis" | + feature_id %in% figure3_asvs ) write_csv(tb0, here("results", "select-asv-sequences-and-taxonomy.csv")) ``` +and a minimal table without the low-prevalence C. hiranonis sequences, +```{r} +tb1 <- tb0 %>% + filter( + ncbi_species != "[Clostridium] hiranonis" | + is.na(ncbi_species) | + feature_id %in% c("ASV4", "ASV62") + ) +write_csv(tb1, here("results", "manuscript-asv-sequences-and-taxonomy.csv")) +``` diff --git a/results/manuscript-asv-sequences-and-taxonomy.csv b/results/manuscript-asv-sequences-and-taxonomy.csv new file mode 100644 index 0000000..5c32573 --- /dev/null +++ b/results/manuscript-asv-sequences-and-taxonomy.csv @@ -0,0 +1,13 @@ +feature_id,sequence,kingdom,phylum,class,order,family,genus,species,ncbi_species +ASV4,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTTAAAGGCTACGGCTCAACCGTAGTAAGCTCCTGATACTGTCTGACTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Peptoclostridium,NA,[Clostridium] hiranonis +ASV10,TACGTAGGCGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGTAGCGAACGGG,Bacteria,Firmicutes,Negativicutes,Selenomonadales,Veillonellaceae,Megamonas,funiformis,NA +ASV20,TACGTAGGTGGCGAGCGTTATCCGGAATGATTGGGCGTAAAGGGTGCGTAGGTGGCAGATCAAGTCTGGAGTAAAAGGTATGGGCTCAACCCGTACTTGCTCTGGAAACTGATCAGCTAGAGAACAGAAGAGGACGGCGGAACTCCATGTGTAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGGCCGTCTGGTCTGGATTCTGACACTGAAGCACGAAAGCGTGGGGAGCAAATAGG,Bacteria,Firmicutes,Erysipelotrichia,Erysipelotrichales,Erysipelotrichaceae,Holdemanella,NA,NA +ASV37,TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCAGCAAGGGTCTGTGGTGAAAGCCTGAAGCTTAACTTCAGTAAGCCATAGAAACCAGGCAGCTAGAGTGCAGGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCCTGCAACTGACGCTCAGTCCCGAAAGCGTGGGGAGCAAATAGG,Bacteria,Firmicutes,Erysipelotrichia,Erysipelotrichales,Erysipelotrichaceae,Erysipelatoclostridium,ramosum,NA +ASV62,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTTAAAGGCTACGGCTCAACCGTAGTAAGCTCCTGATACTGTCTGACTTGAGTGCAGGAGAGGAAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Peptoclostridium,NA,[Clostridium] hiranonis +ASV82,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA +ASV112,TACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCTGTAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAATTGCATTTGTGACTGCAGGACTAGAGTTCATCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCAATGGCGAAGGCAGCCCCCTGGGATGCGACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Proteobacteria,Gammaproteobacteria,Betaproteobacteriales,Burkholderiaceae,Sutterella,massiliensis/stercoricanis/wadsworthensis,NA +ASV233,TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGTGCGTAGGTGGCATGGTAAGTCAGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTTGAAACTGTCATGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTCACTGACACTGATGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Lachnospiraceae,Anaerostipes,caccae,NA +ASV331,TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Ruminococcaceae,Flavonifractor,plautii,NA +ASV843,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGTAAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,NA,NA +ASV1962,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA +ASV2073,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTATTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA