Sailfish for genomic level quantification

[Steven Hill]

Has anyone tried using sailfish to quantify copy number variation throughout a genome? Without diving into the materials and methods of the paper, it seems as though the idea is the same. I'd appreciate any insights.

[Steve Mount]

We have thought about that but not done it. I would guess that making a dummy transcriptome from non-overlapping tiles (perhaps 2 kb.) might be a good first try. 

On Mon, Feb 23, 2015 at 4:46 PM, Steven Hill <hill2...@gmail.com> wrote:

Has anyone tried using sailfish to quantify copy number variation throughout a genome? Without diving into the materials and methods of the paper, it seems as though the idea is the same. I'd appreciate any insights.

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Sailfish is available at http://www.cs.cmu.edu/~ckingsf/software/sailfish/
Citation:
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms
Rob Patro, Stephen M. Mount, and Carl Kingsford
manuscript submitted (2013)
http://arxiv.org/pdf/1308.3700.pdf
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Stephen M. Mount
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Dept. of Cell Biology and Molecular Genetics
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