Do indexes made with cDNA fasta file contain only mRNAs?

Question

[bioinfo]

Hello,

I am using the human index from https://github.com/pachterlab/kallisto-transcriptome-indices/releases to align my data. The index was made using the cDNA fasta file. I know that that means that the index does not contain non coding RNAs. Does the index contain only mRNAs?

Thank you

Answer 1

[dsull]

Correct.

If you want to index rRNA, lncRNAs, etc. then use kb ref on the GTF and genome FASTA file. I recommend doing this because Cell Ranger's reference includes lncRNAs and many noncoding RNAs are polyadenylated.

The index you link to is old (2019) so I wouldn't recommend using that index. Also see here: https://www.r-bloggers.com/2020/01/comparing-ensembl-gtf-and-cdna/