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What is RNAprof?

RNAprof (RNA Profile comparison) is a suite of R and Perl programs for the analysis of RNA-seq profiles that seeks evidence of differential processing events between two RNA-seq experiments.

RNAprof takes as input a set of BAM files obtained from mapping RNA-seq reads onto a reference genome sequence. BAM files must come from two (or more) different experimental conditions, with possible replicates. Optionally, a GFF file identifying gene regions to be analyzed can be provided, otherwise a utility program will generate a GFF file from the BAM files.

Authors: Van Du Tran and Daniel Gautheret.

Latest versions

Program is available for download here.

Output Example

See here an example output of an RNAprof run with the Arabidopsis thaliana NSRab experiment (RNA Biol. 2016, 13:59-67.).


Please cite: Tran Vdu T, Souiai O, Romero-Barrios N, Crespi M, Gautheret D. Detection of generic differential RNA processing events from RNA-seq data. RNA Biol. 2016, 13:59-67.

Update notes

Version 1.2.6
* Fix bug on count average introduced in v1.2.5.
* Improve flexibility with given GFF file.

Version 1.2.5
* Fix pipe bug for unstranded RNA-seq.
* Fix EOF bug in gtf2gff conversion.
* Display count average for each condition in loci.gff.

Version 1.2.4
* Display score (fold-change) in HTML output.
* Remove warning messages for nonstandard SAM flags.

Version 1.2.3
* Improved compatibility with samtools 1.2, 1.3.

Version 1.2.2
* New fix to Mac OS installation.

Version 1.2.1
* Fixed Mac OS installation.

Version 1.2.0
* The XS tag in mapping files is not required any more. The SAM flags
are used. Only properly mapped reads (flags: 0, 16 for single-end;
83, 163, 99, 147 for paired-end) are considered. Reads with wrongly
assigned XS will be rejected.
* RNAprof also works with given unsorted GFF file.
* Introduce a simple check for given GFF file.
* Introduce option --memory for maximum memory per process.
* Improve error handling.
* Improve cluster use.