Module : Features Metadata Extractor - ComputationalSystemsBiology/Single-cell-RNA-seq GitHub Wiki

Module : Features Metadata Extractor

This module extracts information about features from the annotation file.

  • Internal name : featuresmetadataextractor

  • Avalaible : local mode

  • Input Ports :

    • featuresannotation : annotation file (gff, gtf)

  • Output Ports :

    • genesoutput :genes metadata (tsv)

  • Optional parameters :

Parameter Type Description Default Value
genomic.type string Type of the feature to consider, example : exon, gene, transcript exon
attribute.id string ID used as reference to feature Parent
mitochondrial.tag string Tag indicating mitochondrial localization in the annotation file MT
spike.tag string Tag indicating exogenous RNA in the annotation file ERCC
features.file.format string One of : gtf, gff, or gff3 none
  • Configuration example
<step id="exons" skip="false">
        <module>featuresmetadataextractor</module>
        <parameters>
           <parameter>
              <name>genomic.type</name>
              <value>exon</value>
           </parameter>
           <parameter>
              <name>attribute.id</name>
              <value>Parent</value>
           </parameter>
           <parameter>
              <name>mitochondrial.tag</name>
              <value>MT</value>
           </parameter>
           <parameter>
              <name>spike.tag</name>
              <value>ERCC</value>
           </parameter>
           <parameter>
              <name>features.file.format</name>
              <value>gff</value>
            </parameter>
        </parameters>
</step>
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