Adapter_Trimming

Basic Usage

The Adapter_Trimming handler trims adapters off samples. This script utilizes Scythe on paired-end or single-end data. To run Adapter_Trimming, all common and wrapper-specific variables must be defined within the configuration file. Once the variables have been defined, Adapter_Trimming can be submitted to a job scheduler with the following command:

sequence_handling Adapter_Trimming Config

Where Config is the full file path to the configuration file.

Variables

The following are a list of variables that need to be defined within Config. In addition to the handler-specific variables, all common variables must be defined.

Variable	Line	Function
Email	5	Sets an email address for notifications of job status
SEQUENCE_HANLDING	66	The full path to the directory in which sequence_handling is stored
SAMPLE_INFO	69	A list of samples to trim
FORWARD_NAMING	75	Extension for forward files
REVERSE_NAMING	76	Extension for reverse files
PROJECT	79	A name that describes the project you are working on
SCRATCH	82	A directory that will hold results
ADAPTERS	85	A plain text or fasta file with the adapter sequences
PRIOR	89	A prior value for Scythe
THRESHOLD	94	The threshold for quality trimming in Sickle
PLATFORM	97	The platform used for sequencing. This can be found in the output files from Assess_Quality.sh
R Definition	100-102	Define the path to an R installation or load it from a cluster

Output

Quality_Trimming.sh creates trimmed FastQ files for each sample. It also generates trimming statistics to help assess quality both before and after trimming. It is still recommended that Assess_Quality.sh be used for more complete quality assurance. In addition, a list of all trimmed files will be output for use with other scripts.

After the job has run, a list of trimmed FastQ files will be generated for use with read_mapping_start.sh, please view the output file from the job submission to obtain the path to the list.

Dependencies

Adapter_Trimming depends on Scythe to perform the trimming. This is not installed on MSI and must be installed separately. Furthermore, PBS and GNU Parallel are required for basic running.

Next: Quality_Trimming or Read_Mapping