how to get reference genome annotation and refseq_IDmapping.txt from gencode? or generate by myself?

[lu lu]

Hi Zheng,

My RNA-seq data is aligned to Gencode using STAR,  as you mentioned,  the reference genome annotation used should be consistent with the one used in generating RNA-seq bam files.   could I convert by reference annotation gtf file to bed.file directly, and how to get the refseq_ID mapping.txt if I use my gtf file?

Best,

Lu Lu