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
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!
Oh man whoops I should have realized that. But also their tutorial is internally inconsistent I guess!
Thanks!