Question about kallisto indexes

[st4302]

Hello,

I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an index created by concatenating Mus_musculus.GRCm39.cdna.all.fa.gz Mus_musculus.GRCm39.ncrna.fa.gz and then using kallisto index on that file.

I know the v1 kallisto index was created using kb ref but I am not using kb ref for alignment. The command that I will be using to align will be kallisto quant -i mousecdna_ncrna -o mouse_kallisto/MTKO5 -t 4 --rf-stranded MTKO5_R1_001.fastq.gz MTKO5_R2_001.fastq.gz

I am interesting in lncRNAs for my project.

Thank you