Hi,

I am performing RNA-seq analysis on 12 samples. After mapping the reads with Hisat2, I want to count the number of reads using feaureCounts, but I reencountered a problem in reading the gff file downloaded from TAIR. (I also tried downloading it from Ensmbl, but no difference).

featureCounts -p -t exon \
  -a TAIR10_GGF3_genes.gff \
  -o feature.txt \
  erf_2H_A_2.sam erf_2H_A_3.sam \
  erf_2H_A_4.sam erf_2H_H_1.sam \
  erf_2H_H_2.sam erf_2H_H_3.sam \
  WT_2H_A_2.sam WT_2H_A_3.sam \
  WT_2H_A_4.sam WT_2H_H_2.sam \
  WT_2H_H_3.sam  WT_2H_H_4.sam

Running this code results in this error:

Load annotation file TAIR10_GGF3_genes.gff ...  ||
    Failed to open the annotation file TAIR10_GGF3_genes.gff, or its format is incorrect, or it contains no 'exon' features.

So I tried to specify "no exon" in the feature type section:

featureCounts -p -t noexon \
  -a TAIR10_GGF3_genes.gff \
  -o feature.txt \
  erf_2H_A_2.sam erf_2H_A_3.sam \
  erf_2H_A_4.sam erf_2H_H_1.sam \
  erf_2H_H_2.sam erf_2H_H_3.sam \
  WT_2H_A_2.sam WT_2H_A_3.sam \
  WT_2H_A_4.sam  WT_2H_H_2.sam \
  WT_2H_H_3.sam  WT_2H_H_4.sam

Same error:

 Load annotation file TAIR10_GGF3_genes.gff ... |
    Failed to open the annotation file TAIR10_GGF3_genes.gff, or its format is incorrect, or it contains no 'noexon' features.

Of course, my first attempts were without any parameters in the feature type section, but still the same error :___(