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Examples

Single-End RNA-seq

fcount-rs -a annotation.gtf -o counts.txt sample.bam

Paired-End RNA-seq

fcount-rs -p -a annotation.gtf -o counts.txt sample.bam

Stranded Library (e.g., dUTP method)

fcount-rs -p -s 2 -a annotation.gtf -o counts.txt sample.bam

Multi-Threaded Processing

fcount-rs -T 8 -a annotation.gtf -o counts.txt sample.bam

Multiple BAM Files

fcount-rs -a annotation.gtf -o counts.txt sample1.bam sample2.bam sample3.bam

Count Multi-Mapping Reads

fcount-rs -M -a annotation.gtf -o counts.txt sample.bam

With fractional counting:

fcount-rs -M --fraction -a annotation.gtf -o counts.txt sample.bam

Feature-Level Counting

Count at exon level instead of gene level:

fcount-rs -f -a annotation.gtf -o counts.txt sample.bam

Quality Filtering

Require minimum MAPQ of 10 and ignore duplicates:

fcount-rs -Q 10 --ignore-dup -a annotation.gtf -o counts.txt sample.bam