Can I use the transcripts_to_genes.txt file from kallisto for bulk RNA seq data?
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2.3 years ago
bioinfo ▴ 150

Can I use the transcripts_to_genes.txt file (https://github.com/pachterlab/kallisto-transcriptome-indices/releases) from kallisto for bulk RNA seq data? Is it only appropriate for single cell RNA seq?

Thank you

kallisto • 1.1k views
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Is it only appropriate for single cell RNA seq?

Where did you get the idea that this is appropriate for scRNAseq?

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On the link it says that it is for use with kallisto | bustools. This link (https://www.kallistobus.tools/) says that it is a workflow for pre-processing single-cell RNA-seq data.

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First off, kallisto | bustools is 100% appropriate for bulk RNA-seq data. You store the pseudoalignments in a BUS file from which you can do TCC-level/transcript-level/gene-level quantifications.

Secondly, the transcripts_to_gene.txt file is also 100% appropriate for bulk RNA-seq data -- if you mapped using the supplied kallisto index, you can use the corresponding transcripts_to_gene.txt file to aggregate transcripts to the gene-level.

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I see - I read that as usable with kallisto & bustools, but you're right - it refers to the kallisto | bustools pipeline. I'd recommend emailing the authors (Sina/Lior)

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