Exon-level counts via featureCounts

Question

[n_navy]

Hello, I'm doing RNA-seq analyses and now I wanna use edgeR's diffSpliceDGE function, but as I understand I need and exon-level count data because I get the error:

> deu <- diffSpliceDGE(lrt, geneid="GeneID")
Total number of exons:  78932
Total number of genes:  78932
Number of genes with 1 exon:  78932
Mean number of exons in a gene:  1
Max number of exons in a gene:  1
Error in diffSpliceDGE(lrt, geneid = "GeneID") :
  No genes with more than one exon

My current featureCounts codes:

#!/bin/bash

/home/user/subread-2.0.2-Linux-x86_64/bin/featureCounts -p \
 -g gene_id \
 -s 2 \
 -a /home/user/rnaseq/gencode.v47.primary_assembly.annotation.gtf \
 -t exon \
 -o /home/user/rnaseq/fcounts.txt \
 -T 8 /home/user/rnaseq/*.bam \
 -M \
 --fraction \

How can I get the proper format? Thank you.

Answer 1

[GenoMax]

I understand I need and exon-level count data

Then you should use

# Level of summarization

  -f                  Perform read counting at feature level (eg. counting 
                      reads for exons rather than genes).

[n_navy]

When I use -f parameter, Successfully assigned alignments is being extremely low.

[rfran010]

Perhaps you have not also allowed multi-overlapping? (exons from different transcripts of the same gene will overlap each other)