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Old 11-16-2016, 09:19 AM   #1
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Default differences between alignment tools for single cell RNAseq data

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.

Last edited by jspagnuo; 11-17-2016 at 01:01 AM.
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alignment, clustering, rna-seq, single cell

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