Hi all, I'm trying to run a single-cell velocity analysis on hg19 data using kallisto, following along with this tutorial: [https://www.kallistobus.tools/velocity_index_tutorial.html][1]

In the tutorial, the introns file they generate theoretically looks like this, with the familiar looking ENST transcript IDs:

    $ head -4 introns.bed
    chr1	12118	12721	ENST00000456328.2_intron_0_109_chr1_12228_f	0	+
    chr1	12612	13329	ENST00000456328.2_intron_1_109_chr1_12722_f	0	+
    chr1	11948	12287	ENST00000450305.2_intron_0_109_chr1_12058_f	0	+
    chr1	12118	12721	ENST00000450305.2_intron_1_109_chr1_12228_f	0	+

However, mine look like this, though I followed their exact instructions on how to generate the introns.bed.gz file from the UCSC table browser.

     >> head -4 introns.bed
        chr1	12200	12639	uc001aaa.3_intron_0_27_chr1_12228_f	0	+
        chr1	12694	13247	uc001aaa.3_intron_1_27_chr1_12722_f	0	+
        chr1	12200	12672	uc010nxr.1_intron_0_27_chr1_12228_f	0	+
        chr1	12670	13247	uc010nxr.1_intron_1_27_chr1_12698_f	0	+

Because of this, I don't think I am able to continue following along with the tutorial, and also don't imagine my file is correct anyways. Can someone please help me understand a) why I can't get normal-looking transcript IDs for GRCh37 (hg19) from UCSC or b) whether I am just doing something totally wrong or c) whether this is fine and there is a workaround. I am just confused as to what those strange IDs are...

Thanks for the help!

  [1]: https://www.kallistobus.tools/velocity_index_tutorial.html
If you want your transcript IDs to have the ENST identifiers, you should select Ensembl Genes instead of UCSC Genes for the track.