Additional File 3.

Mapping statistics for all sequence libraries. Tables recording the total number of reads in each replicate transcriptome library and the total number and percentage of reads aligned to the reference genome sequence. For differential gene expression analysis, Bowtie alignments were of 35 bp reads, allowing up to three mismatches and only retaining uniquely mapped reads (reads that did not align equally well to more than one genome region). For genome annotation-based analyses, Tophat alignments of combined libraries at each time point were of 50 bp reads, using default parameters. The number of introns identified by each alignment was also recorded.

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Ehrenkaufer et al. Genome Biology 2013 14:R77   doi:10.1186/gb-2013-14-7-r77