comparison single_fastq_filtering.xml @ 10:768883847008 draft

Uploaded

9:c2c69c6090f0

      <when value="true">
   		  <param name="sample_size" type="integer" label="Sample size (number of reads)" help="How many reads should be sampled" value="500000" min="0"/>
      </when>
    </conditional>

    <param type="integer" name="cut_off" label="Quality cut-off" value="10" min="0" help="See below how to correctly set the quality cut-off" />
    <param type="integer" name="percent_above" label="Percent above cutoff" value="95" min="0"
           help="Percentage of bases in the read that must have quality equal to or higher than the cut-off value" />

    <conditional name="trimming">
      <param name="sequence_trimming" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Trim reads"/>
      <when value="false">
        <!-- do nothing here -->

#. Filter by quality      
#. Cutadapt filtering 
#. Sampling (optional)         
#. Interlacing two fasta files

**Quality setting cut-off**

To correctly set quality cut-off, you need to know how the quality is encoded in your fastq file, default
filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below::


      Default filtering cut-off
                |   
                |
                V
      SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................
      ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................

10:768883847008

      <when value="true">
   		  <param name="sample_size" type="integer" label="Sample size (number of reads)" help="How many reads should be sampled" value="500000" min="0"/>
      </when>
    </conditional>

    <param type="integer" name="cut_off" label="Quality cutoff" value="10" min="0" help="See below how to correctly set the quality cutoff" />
    <param type="integer" name="percent_above" label="Percent above cutoff" value="95" min="0"
           help="Percentage of bases in the read that must have quality equal to or higher than the cutoff value" />

    <conditional name="trimming">
      <param name="sequence_trimming" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Trim reads"/>
      <when value="false">
        <!-- do nothing here -->

#. Filter by quality      
#. Cutadapt filtering 
#. Sampling (optional)         
#. Interlacing two fasta files

**Quality setting cutoff**

To correctly set quality cutoff, you need to know how the quality is encoded in your fastq file, default
filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below::


      Default filtering cutoff
                |   
                |
                V
      SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................
      ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................