Introducing subreads featureCounts

What is subreads featureCounts?

subreads featureCounts is a software package for genome annotation and feature counting. It can be used to count reads that map to specific genomic regions such as genes, exons, and promoters. It is designed to be fast and efficient, making it a useful tool for high-throughput sequencing analysis.

Key features

• Annotation: subreads featureCounts can use a variety of annotation formats including GTF, GFF, and BED.

• Compatibility: subreads featureCounts is compatible with many popular alignment tools and file formats including SAM, BAM, and CRAM.

• Speed: subreads featureCounts is designed to be fast and efficient, making it ideal for analyzing large datasets.

• Accuracy: subreads featureCounts uses advanced algorithms to accurately count reads that align to overlapping features.

• Flexibility: subreads featureCounts allows users to customize many aspects of the counting process including minimum and maximum read lengths, strand specificity, and read pair restrictions.

How to use subreads featureCounts

subreads featureCounts can be used from the command line or from within a script. Here is an example of how to count reads from a BAM file using the GTF file for the human genome:

$ featureCounts -a hg19.gtf -o counts.txt -T 8 -p bam *.bam

In this example, the -a parameter specifies the annotation file (hg19.gtf), the -o parameter specifies the output file (counts.txt), the -T parameter specifies the number of threads to use (8), and the -p parameter specifies that the input files are in BAM format.

Conclusion

subreads featureCounts is a powerful tool for genome annotation and feature counting. Its speed, accuracy, and flexibility make it a popular choice for high-throughput sequencing analysis. If you're new to subreads featureCounts, be sure to check out the documentation and tutorials available on the project's website. Happy counting!