RNA2DNAlign evaluates evidence for asymmetric allele distribution in next-gen sequencing reads of DNA and RNA samples from the same individual. RNA2DNAlign requires, as input: genome aligned reads and SNV loci to analyze. Reads from each analysis type and sample must be aligned to the same version of the human genome reference. SNVs may be derived from the reads directly, using, for example, Samtools, or they may be derived from independent sources, such as lists of known annotated variants. Variant positions must correspond to genomic coordinates of the reference genome used for the alignment.

RNA2DNAlign is available as a self-contained binary package for 64-bit Linux systems and as Python source. The pysam package, plus a variety of common third-party python packages including numpy and scipy must be installed to use in Python source form. See the install instructions for more details. The self-contained binary package is appropriate for most Linux users.

Setup:

• Download
• Install

Usage:

• RNA2DNAlign

File Formats:

• Input Files
• Output Files
• Annotation Files

Examples