Hi all,

I have GRCh37 fasta  sequence & GTF  annotation file and ERCC fasta sequence file (but I don’t have ERCC annotation file (GTF)). I want to build genome index file including ERCC sequence using STAR. please help me how to build index file with ERCC? 

Thanks
Cat the fasta files together and then add an entry for each spike-in into the GTF file. Note that you could instead just map against the spike-ins and use `samtools idxstats` to get the counts for the spike-ins. The multimapping rate within the spike-ins and between the spike-ins and the human genome will be very low, so this will produce accurate enough results.