Welcome to the RNAseq read count tool page


This page gives a very brief overview of 3 tools available for counting how many reads overlap with certain genomic features.

The following tools are briefly described and compared here: HTseq-count(part of HTSeq package), FeatureCounts(part of Subread package), ReadCounter. Other tools are available, but I have not tested these and are therefore not included in this page.

    HTseq-count:
  1. First widely accepted counting tool.
  2. Elaborate documentation available: HTseq-count
  3. Help available on forums: SeqAnswers
  4. Written in Python
  5. Link to download:HTseq-count installation
  6. Submitted:HTSeq – A Python framework to work with high-throughput sequencing data

    FeatureCounts:
  1. 10-20 X faster than HTseq.
  2. Automatically sorts .sam/.bam files if needed
  3. Help available on forums: SeqAnswers
  4. Written in C
  5. Link to download: FeatureCounts
  6. Published (Bioinformatics): FeatureCounts paper

    ReadCounter:
  1. Slower than FeatureCounts, but still >10X faster than HTseq
  2. Less ambiguously read counts
  3. Also reports counts per exon/intron.
  4. Reports ambiguously mapped reads for each gene/exon/intron and the number of other genes they map to.
  5. Can used for transcript counts instead of gene counts.
  6. Automatically sorts .sam/.bam files if needed
  7. Written in Java
  8. No installation required, can be run using command line instructions on any operating system (Windows/Mac/Linux).
  9. Link to download:

I created this tool as I wanted to investigate co-expession patterns between introns and exons. Also I required a tool much faster then anything available at the time since we aimed to analyse a large number (4000+) of samples. In the meantime FeatureCounts was published which performs at an unparalelled speed. When I tested this tool, I found it easy to install and in use and would recommend it. If you are interested in a more elaborate analysis of your expression data and would like to investigate the expression of introns and exons I would recommend ReadCounter. HTseq-count is meant to be easy in use for customization, but I personally did not find it easy to achieve my goals and opted to write my own tool. HTseq is well supported by its creators (Simon Anders) who is quick to respond to questions/requests. A large number of other tools can be used to count reads as well, but I never tested them since non of them is significantly faster then HTseq, which I deemed to slow for my purposes. If you have any suggestions or comments feel free to contact me.

How do I use this tool?

ReadCounter is an intuitive command line tool that requires only java to run.

  1. Download readcounter.jar (in linux: wget -O readcounter.jar www.genefriends.org/ReadCounter/ReadCounter/)
  2. run readcounter (for more details see the "About" page)