genophoria

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Monthly Archives: May 2015

How to run kallisto on NCBI SRA RNA-Seq data for differential expression using the mac terminal

Very useful post on Kallisto.

Andrew T McKenzie

Attention Conservation Notice: This post explains how to run the exceptionally fast RNA-seq k-mer aligner kallisto from the Pachter lab on data you download from NCBI’s Short Read Archive, and then analyze it for differential expression using voom/limma. As with everything in bioinformatics, this will likely be obsolete in months, if not weeks.


Kallisto is really fast and non-memory intensive, without sacrificing accuracy (at least, according to their paper), and therefore has the potential to make your life a lot easier when it comes to analyzing RNA-seq data.

As a test data set, I used the very useful SRA DNA Nexus to search the SRA database for a transcriptome study from human samples with 2-3 biological replicates in 2 groups, so that I could achieve more robust differential expression calls without having to download too much data.

I ended up using SRP006900, which is titled “RNA-seq of two…

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