Metadata
The Quick Start introduced the typical pipeline taking paired FASTQ files though to reports, and mentioned the idea of enhancing the reports with sample metadata.
In the following we will show the reports with and without metadata.
As described earlier (see Marker data), metadata.tsv is a table of
metadata based on table S1 in the paper, with 16 columns.
We will use -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 (or --metacols)
meaning show columns 1 to 15 inclusive in the reports (in that order).
Finally, we will use -x 16 or --metaindex 16 to indicate column 16
contains cross references to the sequenced sample filename stems (semi-colon
separated). They will be shown in this order.
This cross referencing idea is key to getting the best results from attaching metadata to your sequenced samples. Here is an abridged representation of the table, showing column one (site or control name), column two (altitude), and finally column 16 which has the filename stems of the sequence data belonging to this row of the table (semi-colon separated list).
#Site |
Altitude |
… |
MiSeq Sample(s) |
|---|---|---|---|
01 |
30 |
… |
Site_1_sample_1; Site_1_sample_2; Site_1_sample_3; Site_1_sample_4; Site_1_sample_5; Site_1_sample_6; Site_1_sample_7; Site_1_sample_8; Site_1_sample_9-2; Site_1_sample_10 |
02 |
55 |
… |
Site_2_sample_1; Site_2_sample_2; Site_2_sample_3; Site_2_sample_4; Site_2_sample_5; Site_2_sample_6; Site_2_sample_7; Site_2_sample_8; Site_2_sample_9; Site_2_sample_10 |
03 |
45 |
… |
Site_3_sample_1; Site_3_sample_2; Site_3_sample_4; Site_3_sample_7; Site_3_sample_8; Site_3_sample_9 |
04 |
20 |
… |
Site_4_sample_1; Site_4_sample_2; Site_4_sample_3; Site_4_sample_3-2; Site_4_sample_4; Site_4_sample_5; Site_4_sample_6; Site_4_sample_8; Site_4_sample_9; Site_4_sample_10 |
05 |
100 |
… |
Site_5_sample_1; Site_5_sample_2; Site_5_sample_4; Site_5_sample_5; Site_5_sample_6; Site_5_sample_8; Site_5_sample_9 |
06 |
5 |
… |
Site_6_sample_1; Site_6_sample_2-2; Site_6_sample_3-1; Site_6_sample_4; Site_6_sample_5-3; Site_6_sample_6; Site_6_sample_7-1; Site_6_sample_8-2; Site_6_sample_9; Site_6_sample_10 |
07 |
105 |
… |
Site_7_sample_1; Site_7_sample_2; Site_7_sample_3; Site_7_sample_5; Site_7_sample_6; Site_7_sample_7; Site_7_sample_8; Site_7_sample_9; Site_7_sample_10 |
08 |
45 |
… |
Site_8_sample_1; Site_8_sample_2; Site_8_sample_3; Site_8_sample_4; Site_8_sample_5-2; Site_8_sample_6; Site_8_sample_7; Site_8_sample_7-2; Site_8_sample_8; Site_8_sample_9 |
09 |
15 |
… |
Site_9_sample_1; Site_9_sample_4-3; Site_9_sample_6; Site_9_sample_7; Site_9_sample_8; Site_9_sample_9; Site_9_sample_10 |
10 |
30 |
… |
Site_10_sample_7; Site_10_sample_8 |
11 |
80 |
… |
Site_11_sample_1; Site_11_sample_2; Site_11_sample_3; Site_11_sample_4; Site_11_sample_5; Site_11_sample_6; Site_11_sample_7; Site_11_sample_8; Site_11_sample_9; Site_11_sample_10 |
12 |
30 |
… |
Site_12_sample_1; Site_12_sample_2; Site_12_sample_3-3; Site_12_sample_4; Site_12_sample_5-3; Site_12_sample_6; Site_12_sample_8; Site_12_sample_9; Site_12_sample_10 |
13 |
300 |
… |
Site_13_sample_1; Site_13_sample_2; Site_13_sample_4; Site_13_sample_5; Site_13_sample_6; Site_13_sample_7; Site_13_sample_8; Site_13_sample_9; Site_13_sample_10 |
14 |
30 |
… |
Site_14_sample_1-2; Site_14_sample_2; Site_14_sample_3; Site_14_sample_4; Site_14_sample_5; Site_14_sample_6; Site_14_sample_10 |
DNA10MIX |
… |
DNA10MIX_undiluted; DNA10MIX_diluted25x; DNA10MIX_bycopynumber |
|
DNA16MIX |
… |
DNA16MIX |
|
NEGATIVE |
… |
NEGATIVE_firstplate; NEGATIVE_secondplate |
Also note that in column one we have listed the numerical site names with
leading zeros giving 01 to 14 to ensure they sort as expected.