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Open Access Highly Accessed Research article

Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species

Emily A Hornett and Christopher W Wheat*

Author Affiliations

Department of Biological Sciences, University of Helsinki, PL 65, Viikinkaari 1, 00014, Helsinki, Finland

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BMC Genomics 2012, 13:361  doi:10.1186/1471-2164-13-361

Published: 1 August 2012

Additional files

Additional file 1:

Table listing the RNA-Seq data used in the de novo transcriptome assemblies (TA) and the basic assembly metrics for each transcriptome assembly.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 2:

Figure depicting the CRR distribution of the single longest TA contig for each CCDS gene, for the different TAs.

Format: TIFF Size: 342KB Download file

Open Data

Additional file 3:

Panels of figures depicting pairwise comparisons of expression data produced when mapping different technical replicates of RNA-Seq Illumina data to varying templates.

Format: TIFF Size: 376KB Download file

Open Data

Additional file 4:

Panels of figures depicting pairwise comparisons of expression data produced when mapping different technical replicates of RNA-Seq Illumina data to varying templates.

Format: TIFF Size: 331KB Download file

Open Data

Additional file 5:

Plot comparing the RNA-Seq expression levels produced from either mapping reads directly to the CCDS dataset, or to a de novo transcriptome assembly.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 6:

Table listing the functional GO and KEGG categories that are significantly (p < 0.05) over- or under-represented in the total list of GRS orthologs of CCDS genes that have a TA hit, compared to the total list of CCDS genes.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 7:

Table listing the functional GO and KEGG categories that are significantly (p < 0.05) over- or under-represented in a list of GRS orthologs of CCDS genes that only have correctly assigned TA hits, compared to the total list of CCDS genes.

Format: XLSX Size: 9KB Download file

Open Data

Additional file 8:

Table listing the functional GO and KEGG categories that are significantly (p < 0.05) over- or under-represented in the list of residuals that equal 0 in a plot of expression levels obtained when mapping TA contigs directly to the CCDS gene set versus mapping the same TA contigs to the GRS dataset (and then using the orthologous genes for comparison purposes).

Format: TIFF Size: 8.6MB Download file

Open Data