RNA-seq analysis in R

Counting reads with SubRead - Solutions

Challenge

1. Redo the counting over the exons, rather than the genes. Use featureCounts --help to find the option you need to use. Make sure featureCounts outputs the results to a new file.

  featureCounts \
      -t exon \
      -g exon_id \
      --primary \
      -a references/Mus_musculus.GRCm38.97.gtf \
      -o counts/MCL1.DL.exons.featureCounts \
      bam/MCL1.DL.bam

2. Redo the counting over genes, allowing for multimapping reads. Compare the results to our intial counts.

You need to add the -M flag to count multimapped reads as well as uniquely mapped reads.

  featureCounts \
      -t exon \
      -g gene_id \
      --primary \
      -a references/Mus_musculus.GRCm38.97.gtf \
      -M \
      -o counts/MCL1.DL.multimapped.featureCounts \
      bam/MCL1.DL.bam