FASTX Clipper is used for removing sequencing adapters and linkers.
- To use FASTX Clipper, upload your data in FASTQ format.
- Resources: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage
All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > fastx_clipper
Use Barcoded.fq as test data.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- Enter the adapter string to clip - CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG
- Leave other parameters in the default states
Expect a FASTQ file fastx_clipper_out.fastq as output.