Package: rnacounter
Welcome!Rnacounterestimates abundances of genes and their different transcripts
from read alignments. Exons and introns can also be quantified.It provides fast read counting in annotated genomic features as well as a simple,
yet efficient solution to the quantification of isoforms from RNA-seq data.
The method used is described in [<ref>].
A typical run is expected to take less than 2 minutes for a 1Gb BAM file from mouse
RNA sequencing, increasing linearly with the BAM size.For all these tasks it only requires a BAM file from a read mapping on the genome,
and a single GTF/GFF file describing the exon structure
such as those provided by Ensembl or GenRep.It is not meant to be used as a library, but through its command-line tool “rnacounter”.The code project is hosted in Github (https://github.com/delafont/rnacounter), GPL-2 licensed.Usage:See “rnacounter –help” and the tutorial athttp://bbcf.epfl.ch/bbcflib/tutorial_rnacounter.html,
also available in the doc/ folder.Minimal example:rnacounter test.bam test.gtfInstallation:First ensure that you have numpy installed, then install rnacounter.
With easy_install:sudo easy_install numpy
sudo easy_install rnacounterOr better yet, with pip:sudo pip install numpy
sudo pip install rnacounterIt installs as a standard Python library but includes the executable
and puts it somewhere in your $PATH. Dependencies will be added
automatically.Check that it works with thetestcommand:rnacounter testIt should display something similar to this:ID  Count   RPKM    Chrom   Start   End     Strand  GeneName        Type    Sense   Synonym
ENSMUSG00000038271  0.0     0.0     chr6    125095258       125111800       1       Iffo1   Gene    .       .
ENSMUSG00000057666  3956.87179487   434612.223694   chr6    125111870       125116485       -1      Gapdh   Gene    .       .
ENSMUSG00000038252  0.0     0.0     chr6    125118026       125141613       -1      Ncapd2  Gene    .       .To uninstall with pip:sudo pip uninstall rnacounterThe code is fully compatible with Python 2.7 and Python 3.Building from source:This allows to modify the Cython source code (rnacounter.pyx) before rebuilding.Clone or download the repository fromhttps://github.com/delafont/rnacounter.You need cython installed (pip install cython).From where rnacounter.pyx lies (rnacounter/rnacounter/), run:sudo python setup.py build_extIt will recompile to create rnacounter.c, and build it.
Then add the executable (rnacounter/bin/rnacounter) to your $PATH,
or install from the package root (rnacounter/) with:sudo python setup.py installDependencies:Tests run with the library versions below, but may work with earlier versions.setuptools 7.0+  (installation)pysam 0.7.5+     (samtools wrapper)numpy 1.6.2+     (efficient numeric arrays)scipy 0.9.0+     (NNLS algorithm)docopt 0.6.1+    (command-line args parsing)cython 0.20+     (translate Python code to C)Testing:Testing files in the testfiles/ folder:
- gapdhKO.bam: alignment on mm9 with only Gapdh covered.
- mm9_3genes_renamed.gtf: extract of the Ensembl GTF with Gapdh, the gene before and the gene after it.
- mm9_Gapdh_renamed.gtf: extract of the Ensembl GTF with Gapdh only.Example:rnacounter testfiles/gapdhKO.bam testfiles/mm9_3genes_renamed.gtf(which is equivalent to what thetestcommand does):rnacounter testThe BAM contains 4041 reads all aligning perfectly on Gapdh (ENSMUSG00000057666) exons,
mostly on ENSMUSE00000487077 but also ENSMUSE00000751942 and ENSMUSE00000886744.
Nothing on other exons, which makes it a good example of badly conditioned input data…The least squares method returns counts on the following transcripts:
ENSMUST00000117757, ENSMUST00000118875, ENSMUST00000147954
and nothing on ENSMUST00000073605, ENSMUST00000144205, ENSMUST00000144588 .Troubleshooting:Any bug report, usage issue or feature request not listed below can be addressed tojulien.delafontaine@epfl.chorwebmaster.bbcf@epfl.ch.