Hi,

I aligned my RNA-Seq reads using STAR on human hg19 genome index build with ENSEMBL annotation (`--sjdbGTFfile` option at the genome index generation). So in my SJ.out.tab file I will have information about the number of reads supporting splice junction as described in STAR manual :

```
column 1: chromosome
column 2: first base of the intron (1-based)
column 3: last base of the intron (1-based)
column 4: strand (0: undefined, 1: +, 2: -)
column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5:AT/AC, 6: GT/AT
column 6: 0: unannotated, 1: annotated (only if splice junctions database is used)
column 7: number of uniquely mapping reads crossing the junction
column 8: number of multi-mapping reads crossing the junction
column 9: maximum spliced alignment overhang
```

In ENSEMBL annotation, there are all types of RNA (mRNA, tRNA, lncRNA,...). But for my research I've to compute the number of uniquely mapped reads crossing only protein-coding genes splice junction. Is there a way to download splice acceptor/donor position in hg19 for protein-coding genes in order to subtract the read count from the `SJ.out.tab` file?

Thanks
HISAT actually comes with a python script that can extract splice sites from a GTF file. So just take your GTF file, extract only the types of entries that you want to include, run `extract_splice_sites.py` on the results and then intersect the results appropriately.