RNA-seq reads mapping on reference genome

Question

[Shahzad]

Dear Friends I want some help regarding mapping my sequencing reads(RNA) on a reference genome. I have RNA-seq data which I want to align on a available reference genome. Problem is that the only "Reference genome" is available on a database as multiple BACs sequencing files. Please guide me how can I use these reference sequences as reference genome.

Thank you

[GenoMax]

You can combine the BAC sequences into a multi-fasta format file. This becomes your "genome". Create indexes for the genome file by an aligner you would like to use (since this is RNAseq data you would want to use a splice aware aligner e.g. STAR, BBMap, HISAT2 etc). Then align your data.

[Shahzad]

@genomax2 Dear genomax2 Thank you for your reply. How make annotation file for this genome?