From 89ec1b00663e71017e6f1fcd5fcaf1e628026517 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Mon, 25 Apr 2022 07:56:09 -0700 Subject: [PATCH] Converted tables --- 0_RawData/README.md | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/0_RawData/README.md b/0_RawData/README.md index f15d9a7..126019e 100644 --- a/0_RawData/README.md +++ b/0_RawData/README.md @@ -1,17 +1,15 @@ # Raw Sequences # Note: -Due to file storage issues (files being too large) I've implented protocols to move them. +Raw FASTQ files are too large and are stored on NCBI/EBI. This page is mostly the metadata. SRA:SRP021107 BioProject:PRJNA196801 ## Files +sample_metadata.txt : Metadata for both the bulk and viral raw reads. ## Directories -* 0_Bacteria : Bulk metagenomics for which we assembled bacterial genomes -* 1_Viral : VLPs were seperated and sequenced. - ## Scripts ## Description @@ -22,13 +20,22 @@ 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 | -SRR828645 - BLS020308_1014-01 - Day 182 - Week 1 -SRR828661 - BLS020309_1014-02 - Day 852 - Week 2 -SRR828660 - BLS020310_1014-03 - Day 882 - Week 3 +SRR828661 - BLS020309_1014-02 - Day 852 - Week 2 +SRR828660 - BLS020310_1014-03 - Day 882 - Week 3 ### Viral Metagenomics +See Fig 1A & Table S1 (note there is a typo for day 851-2) +Unfortunately Table S1 has the '# of reads' which appears to be after QC, as they do no match raw reads. +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