This section contains the following intermediate and result files:
To use this pipeline you need to know the primers that has been used and then seperate them by markers. The data we use is seperated in 4 different kind of markers, they are presented in this table.
| Markers | #I7: 1 – 12 | #I7: 13 – 24 | #I7: 25 – 36 | #I7: 37 – 48 |
|---|---|---|---|---|
| I5: 1 – 8 | ITS locatie 1 21022-375801-001 NI030 | ITS locatie 3 21022-375801-003 NI032 | CO1 locatie 1 21022-375801-001 NI057 | ITS nioo locatie 1 21022-375801-001 NI059 |
| I5: 9 – 16 | ITS locatie 2 21022-375801-002 NI031 | ITS locatie 4 21022-375801-004 NI033 | 18s locatie 1 21022-375801-001 NI058 | 18s nioo locatie 1 21022-375801-001 NI060 |
| I5: 17 – 24 | 16s locatie 1 21022-375801-001 NI034 | 16s locatie 3 21022-375801-003 NI036 | ||
| I5: 25 – 32 | 16s locatie 2 21022-375801-002 NI035 | 16s locatie 4 21022-375801-004 NI037 |
It is important to seprate the data before u run the pipeline. In this case we are ging to seperate the data by ITS markers: NI030, NI031, NI032, NI033
To seperate the data:
find . -name "*NI030*" -exec mv -t ./ITS {} +
Where "*NI030*" is the marker that we wanted to move to ./ITS directory.
Use this to move all needed data with the right markers to a specific directory. This will be the data that we will be using for this pipeline.
To use the server we need to set up the data on the MaaS server. To do so use scp
scp *.gz ubuntu@145.136.253.38:winny.thoen/Data/
Where *.gz are all the files within the current directory and ubuntu@145.136.253.38:~/winny.thoen/Data/ is the directory on the MaaS server. It is not possible to place your data from a local computer in your specific account on the server. To do so de data can be moved from ~/winny.thoen/Data to /home/winny.thoen/arise-metabarcoding-biodiversity/data/raw_sequencesNovaSeq. Where winny.thoen is the personal account where the data needs to be stored. To move the data:
sudo mv *.gz /home/winny.thoen/arise-metabarcoding-biodiversity/data/raw_sequencesNovaSeq
If the data is to big, mv doesn’t work. Use find:
sudo find . -name '*gz*' -exec mv {} /home/winny.thoen/arise-metabarcoding-biodiversity/data/raw_sequencesNovaSeq \;
After moving the data check the permissions before using the dada2 pipeline. If necessary change the permissions using chmod.