Creating a custom adapters.fa file¶

The sequencing company should already trim the adaptes sequence. Therefore , what is usually left to trim is the sequencing primer sequence.

The overrepresented sequences typically dont align very well to the genome , so these sequences are majorly lost during alignment.

Create the adapters.fa in your local data folder
- Open a bash terminal and move to the location where you have the data you would like to mount in the pipeline (fastq files)
```
cd /data
```
- Create the adapters.fa file customized to your dataset.
```
nano adapters.fa
```
- Inside the nano editor , edit the file as follows:
```
> \> Sequence1
>
> Sequencing primer sequence
>
```
- Ctrl-O save , Ctrl-X and quit the editor
Note

Do not put empty lines in the text file, otherwise BBDuk might yield an error about not finding the adapters.fa file.!
Run again the container and it will automatically look for that file (adapterfile.fa) in the data folder .

SATAY pipeline at Delft :)