featureCounts problem in reading Gff

Question

[Beatrice]

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 :___(

[Pierre Lindenbaum]

what is the output of

grep exon -m10 TAIR10_GGF3_genes.gff

?

[Beatrice]

That's the output, so apparently I have the exon. Anyway, after running grep command the featureCounts worked, even though I didn't change a thing.

THANK YOU

Chr1    TAIR10  exon    3631    3913    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    3996    4276    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    4486    4605    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    4706    5095    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    5174    5326    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    5439    5899    .   +   .   Parent=AT1G01010.1
Chr1    TAIR10  exon    8571    8737    .   -   .   Parent=AT1G01020.1
Chr1    TAIR10  exon    8417    8464    .   -   .   Parent=AT1G01020.1
Chr1    TAIR10  exon    8236    8325    .   -   .   Parent=AT1G01020.1
Chr1    TAIR10  exon    7942    7987    .   -   .   Parent=AT1G01020.1

[WouterDeCoster]

Did you download and open the file on a windows machine first?

[WouterDeCoster]

By the way, if you type the beginning of a file or directory and then use the tab key then linux will (try to) complete the rest of the name - you don't have to type filenames all by hand.