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This article is part of the supplement: Proceedings of the Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2012)

Open Access Proceedings

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments

Ekaterina E Khrameeva12* and Mikhail S Gelfand12

Author Affiliations

1 Institute for Information Transmission Problems, Russian Academy of Sciences, 19 Bolshoy Karetny per., Moscow, 127994, Russia

2 Faculty of Bioengineering and Bioinformatics, Moscow State University, 1-73 Leninskie gory, Moscow, 119991, Russia

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BMC Bioinformatics 2012, 13(Suppl 6):S4  doi:10.1186/1471-2105-13-S6-S4

Published: 19 April 2012

Additional files

Additional file 1:

Supplementary figure S1. Correlation of per-nucleotide coverage profiles between all pairs of sequencing experiments for an unfiltered set of single-exon genes (1074 genes). All notations are as in Figure 1.

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Additional file 2:

Supplementary figure S2. Single-exon gene coverage distribution averaged over genomic/mRNA sequencing experiments on Illumina/SOLiD platforms.

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Additional file 3:

Supplementary figure S3. Distribution of linear model fitting coefficients calculated for gene coverage profiles and averaged over genomic/mRNA sequencing experiments on Illumina/SOLiD platforms.

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Additional file 4:

Supplementary figure S4. Correlation of per-nucleotide coverage profiles between all pairs of sequencing experiments normalized for the 5' - 3' coverage non-uniformity. Notations are similar to those in Figure 1.

Format: PDF Size: 80KB Download file

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Additional file 5:

Supplementary figure S5. Single-exon gene coverage distribution over gene length after normalization for mappability profiles. Points of different color represent different experiments grouped by laboratory.

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Additional file 6:

Supplementary figure S6. Additional information about 117 compared mRNA and genome high-throughput sequencing experiments. Experiments are clustered by similarity of single-exon gene coverage profiles as in Figure 1.

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Open Data