I was wondering whether there were any major differences in the readout from single-cell RNAseq reads aligned with traditional short-read alignment tools like Bowtie2 vs a pseudoaligner like Kallisto.
I wanted to leverage the speed of pseudoalignment and use the transcript-compatability counts (TCC) to decrease the alignment bottleneck when dealing with 50,000 cell libraries.
I was told earlier today that Kallisto and clustering on a TCC matrix would produce spurious results, however I'm not convinced given the results in the Ntranos, 2016 paper in Genome Biology.
I wanted to leverage the speed of pseudoalignment and use the transcript-compatability counts (TCC) to decrease the alignment bottleneck when dealing with 50,000 cell libraries.
I was told earlier today that Kallisto and clustering on a TCC matrix would produce spurious results, however I'm not convinced given the results in the Ntranos, 2016 paper in Genome Biology.