From c94aecf448c79bf43e7b07a44b32f8c3a69abba5 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Mon, 25 Apr 2022 08:05:31 -0700 Subject: [PATCH] Converted tables --- 0_RawData/README.md | 62 +++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 33 deletions(-) diff --git a/0_RawData/README.md b/0_RawData/README.md index 126019e..9252c5a 100644 --- a/0_RawData/README.md +++ b/0_RawData/README.md @@ -19,14 +19,14 @@ For 8 time points two seperate viral metagenomic read runs were done. So there a For more information on the metadata and how samples were collected see orginal manuscript. + ### Bacteria (Bulk Metagenomics) See Fig S2 from Minot 2013 paper for days. | SRA | SampleID | Day | Week | | ------- | ----------------- | ------- | ---- | |SRR828645| BLS020308_1014-01 | 182 | 1 | - -SRR828661 - BLS020309_1014-02 - Day 852 - Week 2 -SRR828660 - BLS020310_1014-03 - Day 882 - Week 3 +|SRR828661| BLS020309_1014-02 | 852 | 2 | +|SRR828660| BLS020310_1014-03 | 882 | 3 | ### Viral Metagenomics See Fig 1A & Table S1 (note there is a typo for day 851-2) @@ -34,33 +34,29 @@ Unfortunately Table S1 has the '# of reads' which appears to be after QC, as the I followed the labels from Sample_ID where 'd00-1' where the first digit is the week. Day zero is 00, and week 1 is 01-5. The second digit is the day of the week. -SRA Sample_ID Day Replicate -SRR829033 BLS020813_d00-1 0 1 -SRR829867 BLS020814_d00-2 0 2 -SRR935337 BLS020815_d01-1 180 1 -SRR935339 BLS020816_d02-1 181 1 -SRR935340 BLS020817_d03-1 182 1 -SRR935341 BLS020818_d03-2 182 2 -SRR935342 BLS020819_d04-1 183 1 -SRR829034 BLS020820_d05-1 184 1 -SRR935364 BLS020821_d11-1 851 1 -SRR935366 BLS020822_d11-2 851 2 -SRR935367 BLS020823_d12-1 852 1 -SRR935361 BLS026407_d12-2 852 2 -SRR935348 BLS020824_d13-1 853 1 -SRR935349 BLS020825_d13-2 853 2 -SRR935350 BLS020826_d14-1 854 1 -SRR935351 BLS020827_d15-1 855 1 -SRR935352 BLS020828_d21-1 879 1 -SRR935354 BLS020829_d21-2 879 2 -SRR935356 BLS020830_d22-1 880 1 -SRR935363 BLS020831_d22-2 880 2 -SRR935357 BLS020832_d23-1 881 1 -SRR935358 BLS020833_d23-2 881 1 -SRR935359 BLS020834_d24-1 882 1 -SRR935360 BLS020835_d25-1 883 1 - -Note: Table S1 does not match up with the data they uploaded or from Fig.1 of the Minot et al dataset. -For example day 851 should be in duplicate based on Fig 1. and sequences uploaded on SRA but is only one in Table S1. So I do not trust Table S1 -The pattern for d##_# works out to be d- - +| SRA | SampleID | Week | Day | Replicate | +|-----------|-----------------|------|-----|-----------| +| SRR829033 | BLS020813_d00-1 | 0 | 0 | 1 | +| SRR829867 | BLS020814_d00-2 | 0 | 0 | 2 | +| SRR935337 | BLS020815_d01-1 | 1 | 180 | 1 | +| SRR935339 | BLS020816_d02-1 | 1 | 181 | 1 | +| SRR935340 | BLS020817_d03-1 | 1 | 182 | 1 | +| SRR935341 | BLS020818_d03-2 | 1 | 182 | 2 | +| SRR935342 | BLS020819_d04-1 | 1 | 183 | 1 | +| SRR829034 | BLS020820_d05-1 | 1 | 184 | 1 | +| SRR935364 | BLS020821_d11-1 | 2 | 851 | 1 | +| SRR935366 | BLS020822_d11-2 | 2 | 851 | 2 | +| SRR935367 | BLS020823_d12-1 | 2 | 852 | 1 | +| SRR935361 | BLS026407_d12-2 | 2 | 852 | 2 | +| SRR935348 | BLS020824_d13-1 | 2 | 853 | 1 | +| SRR935349 | BLS020825_d13-2 | 2 | 853 | 2 | +| SRR935350 | BLS020826_d14-1 | 2 | 854 | 1 | +| SRR935351 | BLS020827_d15-1 | 2 | 855 | 1 | +| SRR935352 | BLS020828_d21-1 | 3 | 879 | 1 | +| SRR935354 | BLS020829_d21-2 | 3 | 879 | 2 | +| SRR935356 | BLS020830_d22-1 | 3 | 880 | 1 | +| SRR935363 | BLS020831_d22-2 | 3 | 880 | 2 | +| SRR935357 | BLS020832_d23-1 | 3 | 881 | 1 | +| SRR935358 | BLS020833_d23-2 | 3 | 881 | 2 | +| SRR935359 | BLS020834_d24-1 | 3 | 882 | 1 | +| SRR935360 | BLS020835_d25-1 | 3 | 883 | 1 |