The remaining read number and ratio compared to raw reads were calculated for each mapping step (Table S3 in Supplement 1). Control and alcoholic samples had similar ratios from each step though there were some individual variations. Based on the quality filter, about 20% raw reads were filtered out, and the second filter for non-coding RNAs and adaptors left approximately 53% raw reads. After TopHat mapping, the unique mapped reads were generated with about 41% mappability.
