I am using a pipeline (http://churchill-lab.github.io/emase-zero/) to create organism-specific diploid transcriptomes to align RNAseqs to and then quantify with allele specific expression. They suggest:

Note: We highly recommend adding poly-A tail to the alignment target sequences (transcripts) when you build bowtie index. We usually add (R-1)-long poly-A tails where R is the read length.

Is there an available tool that accomplishes this?