Building a cDNA and intron index for Kallisto/Bustools Single Cell Velocity for hg19

Question

[ekofman]

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!

Answer 1

[dsull]

If you want your transcript IDs to have the ENST identifiers, you should select Ensembl Genes instead of UCSC Genes for the track.

[ekofman]

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

Thanks!