Sequences and quality scores were extracted from image files using Firecrest, Bustard, and GERALD software. Sequences were aligned to the Mus musculus genome (2007, mm9; NCBI Build 37) using Bowtie (http://bowtie-bio.sourceforge.net; version 0.12.7) (Langmead et al., 2009) permitting multi-alignment and allowing up to 2-mismatches. Ambiguous alignments were resolved using the Spliced Paired-end Aligner Perl script (Brooks et al., 2011). Robust assembly of novel transcripts and a complete analysis of cocaine-induced alternative splicing requires greater transcript coverage and read depth than we obtained (Trapnell et al., 2010).
