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. 2011 Oct 20;12:516. doi: 10.1186/1471-2164-12-516

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Copyright ©2011 Odawara et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Plots to assess the effect of the parameter 'Max multihits' (X-axis). 'Max multihits' is a TopHat parameter that indicates how many times one tag is permitted to be aligned. (a) Number of genes found by RNAseq (Y-axis) against 'Max multihits'. (b) Spearman's correlation between microarrays (GSM23372, GSM161670, and GSM246123) and RNAseq. (c) Y-axis indicates how many splicing sites found in TopHat were included in known genes or FPKM > 0 genes. (d) Histogram showing the distribution of FPKM. As the number of permitted 'Max multihits' increased, the quantity of genes with small FPKM values increased (black arrows).