Can I use the transcripts_to_genes.txt file from kallisto for bulk RNA seq data?
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
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Where did you get the idea that this is appropriate for scRNAseq?
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.
I see - I read that as usable with kallisto & bustools, but you're right - it refers to the
kallisto | bustoolspipeline. I'd recommend emailing the authors (Sina/Lior)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.txtfile is also 100% appropriate for bulk RNA-seq data -- if you mapped using the supplied kallisto index, you can use the correspondingtranscripts_to_gene.txtfile to aggregate transcripts to the gene-level.