Question: RNAseq read counts generated by FeatureCounts
0
gravatar for adeler001
23 days ago by
adeler0010
adeler0010 wrote:

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?

rnaseq featurecounts • 66 views
ADD COMMENTlink modified 23 days ago by James W. MacDonald52k • written 23 days ago by adeler0010

Cross-posted: https://www.biostars.org/p/408898/

ADD REPLYlink written 23 days ago by Kevin Blighe390
Answer: RNAseq read counts generated by FeatureCounts
2
gravatar for James W. MacDonald
23 days ago by
United States
James W. MacDonald52k wrote:

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.

ADD COMMENTlink written 23 days ago by James W. MacDonald52k

ok thank you for answering

ADD REPLYlink written 9 days ago by adeler0010
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