questions regarding building index including introns

[jingzhangorg]

Hello,

I am new to kallisto and I am learning to use it to analyze single nuclei RNA-seq data, where I found a lot of reads from the introns.

I followed the instructions from https://www.kallistobus.tools/velocity_index_tutorial.html
and also compared to download the prebuilt index from https://www.kallistobus.tools/velocity_tutorial.html

The downloaded cDNA_introns.t2g.txt file seems to be correct that each intron has a unique id with correct mapping to genes.
ENST00000463325.1056070-I ENSG00000184319 RPL23AP82

The index I built myself seems to be strange. somehow the introns_tr2g.txt file does not show the correct intron ID.
ENST00000456328.2 ENSG00000223972.5 DDX11L1

And the code in the tutorial does not seem to output the intron ID but rather the transcript ID.
"awk 'NR==FNR{a[$1]=$2; b[$1]=$3;next} {$2=a[$1];$3=b[$1]} 1' tr2g.txt introns_transcripts.txt > introns_t2g.txt"

Would you please suggest on this? Thank you very much