Gene-level visualisation of RNA-seq reads mapped to the chicken genome. Annotated CLC Bio Genomic Workbench views of chicken chromosome Z (A) and 4 (B) showing the loci around homologues of CCL19 (ENSGALG00000028256) (A) and PYURF (ENSGALG00000026229) (B). Each panel shows tracks for genes (labeled with Galgal4—annotated names), untranslated regions (UTR), coding sequences (CDS) and mRNA transcripts. Locations of unannotated NCBI Galgal5 Refseq genes LOC 1008571891 (A) and LOC422513 (B) are indicated. RNA-seq reads from untreated and IFN-treated CEF (6 h, 1000 units) are shown mapped to the genome in the uppermost and lowest tracks, respectively, in each panel (totals mapped to the chromosome are indicated to the left of these tracks). The levels of basal and peak RNA-read mappings are shown to the right of the tracks under “Scale”. Comparison of these figures in conjunction with the size of the peaks allows visual estimates of the levels of differential expression for individual exons (which can be compared with the formal numerical analyses). For instance, IL11RA (A) as well as CCGN2 and HERC3 (B) show no significant regulation by IFN. In contrast, CCL19 and unannotated LOC100857191 in (A) show significant upregulation (96-fold—but with an FDR of 0.031 it fell outside the cut-off for Kal’s analysis and, because of its very low basal expression, was not returned by Baggerly’s). In (B) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5.