rsem-prepare-reference --allele-to-gene-map <file> (file information required)

[Anindyajit Banerjee]

--allele-to-gene-map <file>

Use information from <file> to provide gene_id and transcript_id information for each allele-specific transcript. Each line of <file> should be of the form:

gene_id transcript_id allele_id

with the fields separated by a tab character.

This option is designed for quantifying allele-specific expression. It is only valid if '--gtf' option is not specified. allele_id should be the sequence names presented in the Multi-FASTA-formatted files.

I tried to look for allele to gene map option, but I found some difficulties in preparing/building the reference file. 

rsem-prepare-reference --allele-to-gene-map <file> reference_fasta_file(s) reference_name

From where to obtain this <file> or from which Multi-FASTA-formatted files we can obtain 

gene_id transcript_id allele_id.

Please suggest

Thanks

AB