Ad hoc code for Alu sequence analysis.
Software versions:
--Python 3.6
--R 3.4.4
--featureCounts 1.6.1
--STAR 2.5.3a
The first analyses plots the Alu expression distribution for RPE vs. non-RPE associated genes. 'geneAluCount_ExampleScript.sh' illustrates the process. The second analysis searches for multi-aligned reads where all alignments map to the same Alu subfamily. 'multiMap_ExampleScript.sh' outlines this procedure.