FeatureCounts count reads per gene (Including Introns)

Question

[paulranum11]

Hi Everyone,

I am using featureCounts to count the number of reads mapping to genes.

        featureCounts -a $myGTF \
                  -o counted_output \
                  -R BAM Aligned.sortedByCoord.out.bam \
                  -T $NUMCORES \
                  -M

The above bash command works counting reads that map to the exonic sequences of each genes annotated in the $myGTF file.

My question is, how can I get featureCounts to also count reads mapping to intronic sequences? It is unclear to me how to achieve this from the documentation but it might be through some combination of -O and -f.

Thanks!

[GenoMax]

If you can get/create an annotation file with intron features, you can then count using that file with -t intron option.

Answer 1

[ATpoint]

Alternatively make a custom reference in featureCount's SAF format (see manual for details) to include introns.

[paulranum11]

This is what i ended up doing. It was easy to make this SAF format file using biomart from ensembl.org. For future readers the columns to include for this format are: GeneName, Chromosome, GeneStart, GeneEnd, Strand

Note that the column names header needs to be removed before the SAF file is used with featureCounts.