Delaney Sullivan

Can you show us the "kb ref" (index) and "kb count" (quantification) commands you're using?

No cDNA species are omitted and you should not be observing such results (as they contradict the results of numerous benchmarks performed in the literature). Further, it is not true...

Thanks the for the additional information. That Ensembl FASTA file does not contain any non-coding RNAs. Those will be missing (there are a little over 20,000 of those genes).

I recommend using our kb tool to create indices: https://www.kallistobus.tools/kb_usage/kb_usage.html Install kb-python and then download the genome primary assembly and GTF file to create a transcriptome index. Alternately, you can...

No, you will not be getting the same exact count matrix. When you do pseudoalignment with introns included, your numbers will be different.

Your index is different. Some reads that couldn't map anywhere with a cDNA-only index will now map somewhere when you include introns. Some reads that mapped to a transcript with...

Yes, kallisto can do allele-specific expression; just put the two transcripts (one for each of the two alleles) in the transcriptome index. You'll get a TPM value for each transcript....

The kb ref command is designed to build a cDNA fasta when provided with a raw genome fasta. As you already have the cDNA fasta, the "kallisto index" command is...

See here: https://github.com/pachterlab/kb_python/issues/68 Essentially, a second round of bustools correct is being run. Consider this mostly an experimental feature -- I see no reason to do this in almost all...

Also, unrelatedly, I know BD Rhapsody WTA comes with a whitelist (it's essentially three different whitelists) and it should probably work the same for your version of BD Rhapsody. See...