diff --git a/0_RawData/README.md b/0_RawData/README.md index 9252c5a..7408c6d 100644 --- a/0_RawData/README.md +++ b/0_RawData/README.md @@ -6,7 +6,7 @@ SRA:SRP021107 BioProject:PRJNA196801 ## Files -sample_metadata.txt : Metadata for both the bulk and viral raw reads. +SraRunInfo.txt : Metadata for both the bulk and viral raw reads. ## Directories @@ -16,6 +16,7 @@ sample_metadata.txt : Metadata for both the bulk and viral raw reads. One healthy individual was sampled at 16 time points. For 3 time points bulk metagenomics was sequenced (bacteria metagenomics) and for all 16 time points viral metagenomics was completed. For 8 time points two seperate viral metagenomic read runs were done. So there are 24 viral sequence runs. +See full SRA info (with added in days and replicate) in the file SraRunInfo.txt For more information on the metadata and how samples were collected see orginal manuscript. @@ -31,6 +32,10 @@ See Fig S2 from Minot 2013 paper for days. ### 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. +For example sample SRR829867 has 18020339 reads but no day has this number in Table S1. +(For more information I've uploaded a multiqc file on the raw FASTQ files). + +#### How I assigned metadata 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.