Additional file 11: Table S7. of Errors in RNA-Seq quantification affect genes of relevance to human disease

Novel differentially expressed MMGs. The 672 differentially expressed MMGs that do not contain any genes identified as differentially expressed by the stage 1 analysis. Can be downloaded from [43]. (XLSX 67 kb

Additional file 3: Figure S2. of Errors in RNA-Seq quantification affect genes of relevance to human disease

General characteristics of second problematic group. Boxplots comparing the length of the shortest exon, the length of the longest exon, the mean exon length, the total number of exons, the transcript length, transcript percentage GC, the number of reads overlapping from the STAR alignment and the number of reads overlapping the TopHat alignment for a group of genes where HTSeq underestimates, Cufflinks overestimates and Sailfish is accurate. (JPEG 581 kb

Additional file 8: Table S4. of Errors in RNA-Seq quantification affect genes of relevance to human disease

Counts of multi-map groups (MMGs) from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to MMGs. Can be downloaded from [43]. (XLSX 876 kb

Additional file 5: Figure S4. of Errors in RNA-Seq quantification affect genes of relevance to human disease

General characteristics of third problematic group. Boxplots comparing the length of the shortest exon, the length of the longest exon, the mean exon length, the total number of exons, the transcript length, transcript percentage GC, the number of reads overlapping from the STAR alignment and the number of reads overlapping the TopHat alignment for a group of genes where HTSeq underestimates, Cufflinks and Sailfish are accurate but the use of the --multi-read-correct parameter in Cuffinks results in underestimation. (JPEG 575 kb

Additional file 4: Figure S3. of Errors in RNA-Seq quantification affect genes of relevance to human disease

General characteristics of third problematic group. Boxplots comparing the length of the shortest exon, the length of the longest exon, the mean exon length, the total number of exons, the transcript length, transcript percentage GC, the number of reads overlapping from the STAR alignment and the number of reads overlapping the TopHat alignment for a group of genes where HTSeq underestimates, Cufflinks and Sailfish are accurate. (JPEG 576 kb

Additional file 9: Table S5. of Errors in RNA-Seq quantification affect genes of relevance to human disease

EdgeR results from unique counts. Differential expression results calculated by edgeR for gene counts produced by the stage 1 analysis. Can be downloaded from [43]. (XLSX 2159 kb

Additional file 7: Table S3. of Errors in RNA-Seq quantification affect genes of relevance to human disease

Unique counts from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to genes using STAR and HTSeq. Can be downloaded from [43]. (XLSX 5833 kb

Additional file 10: Table S6. of Errors in RNA-Seq quantification affect genes of relevance to human disease

EdgeR results from MMGs. Differential expression results calculated by edgeR for MMG counts produced by the stage 2 analysis. Can be downloaded from [43]. (XLSX 428 kb

Additional file 13: Table S9. of Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

Mapping locations of the pig CAGE CTSS to the pig genome: uniquely mapped subset (BED). Table contains the following columns (left to right): chromosome, start, end, pig CAGE CTSS ID (strand-specific), number of tags in the CTSS and strand. The first three and sixth columns refer to the mapped locations of the pig CAGE CTSS (as identified by the ID in column 4) onto the pig genome. The set of pig CAGE CTSS reported includes only the uniquely mapped pig CAGE tags. (TSV 3840 kb

Additional file 1: Figure S1. of Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

FANTOM5 promoter comparative analysis framework. FANTOM5 promoters were extended from 400 bases upstream to 100 bases downstream of their main TSS. Orthologous genomic regions were extracted for all genes within the target genome –orthologs between the species the FANTOM5 promoters belong to (human/mouse) and that of the target genome (pig/human/mouse). These regions were extracted as 2.1 Kb windows containing 2 Kb upstream and 100 bp downstream from each orthologous genes’ 5’-end. Promoters mapping to at least one known orthologous region were reported with their mapping locations, while the remaining set of promoters were mapped to the whole target genome (repeat-masked). The set of uniquely mapped promoters is reported with their genomic locations. The multimapped promoters were filtered based on the score ratio of the top two best hits -the top hit was considered to be uniquely mapped if the score ratio (s2/s1) between the second hit (s2) and the first (s1) was below 0.95. Failing the score ratio criteria, one of the two top hits was considered a single hit whenever it was located on a chromosome and all other hits were located on unplaced scaffolds. The unmapped promoters were re-aligned (2nd run - see methods) and the same procedure was followed to report the uniquely mapped promoters. Two sets of genes were extracted from the final set of unmapped FANTOM5 human promoters to the pig genome for GO terms enrichment analysis (see text): the set of genes with at least one FANTOM5 promoter unmapped (referred to as genes_tss) and the set of genes with all associated FANTOM5 promoters unmapped (referred to as genes_none). (PDF 259 kb