Converted tables

0_RawData/README.md

@@ -19,48 +19,44 @@ 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)
 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
-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<week><day of week>-<replicate>
-
+| 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         |