RNAseq read counts generated by FeatureCounts
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adeler001 • 0
@adeler001-21743
Last seen 2.8 years ago
Canada

Hello I used FeatureCounts to do the read counts for my RNAseq data . Do the read counts FeatureCounts provide an average or absolute total of all the reads of the exons per gene ? Is there any way to get the read count for a specific exon in a gene?

featurecounts RNAseq • 2.1k views
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@james-w-macdonald-5106
Last seen 3 days ago
United States

This is covered in the help page for featureCounts:

useMetaFeatures: logical indicating whether the read summarization
          should be performed at the feature level (eg. exons) or
          meta-feature level (eg. genes). If ‘TRUE’, features in the
          annotation (each row is a feature) will be grouped into
          meta-features, using their values in the ‘GeneID’ column in
          the SAF-format annotation file or using the ‘GTF.attrType’
          attribute in the GTF-format annotation file, and then reads
          will be assiged to the meta-features instead of the features.
          See below for more details.

And as mentioned, there are more details in the Details section.

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ok thank you for answering

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