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cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
- To use cutadapt, import your data in FASTQ or fastq.gz format.
- Resources: http://code.google.com/p/cutadapt/
Use illumina.fastq or illumina.fastq.gz from the directory above as test input.
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.
- Default parameters only, no further configuration needed.
Expect a text file named outputForCutadapt.txt with a summary of the clipped sequences and the modified FASTQ file (output.fastq) as output.