Commit 82a7b613 authored by Jerome Mariette's avatar Jerome Mariette
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add cutadapt documentation

parent 5efdb254
......@@ -8,14 +8,14 @@
From the <a href=''>cutadapt site</a> :
cutadapt is used to remove 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.
<li>input file: This program accepts fastq files as input.</li>
<li>qual file list: If a fasta file is used as input a qual file can be provided (has to be named input_file.qual or input_file.fasta.qual).</li>
<li>ng6cfg file: The NG6 run config file the analyse belongs to.</li>
<li>project id: The NG6 project id the analyse belongs to.</li>
Outputs a cleaned file in fastq format and a log file.
<li>min length: Discard trimmed reads that are shorter than LENGTH,</li>
<li>max length: Discard trimmed reads that are longer than LENGTH,</li>
<li>error rate: Maximum allowed error rate,</li>
<li>options: Options for cutadapt ex: -a adaptors,</li>
<li>analyse name: The analyse name to display in ng6,</li>
<li>analyse description: The analyse description to display in ng6,</li>
<li>results archive name: The results archive name to display in ng6.</li>
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