Transcript assembling and annotation from RNASeq data. The figure shows a region of the chromosome 7. Panel A: reads aligned in this region; a small window of the total mapped reads is shown (bottom panel); the relative coverage (logarithmic scale) is depicted as a sky-line on the panel. Each vertical dash represents a read. Reads aligned with the plus strand of the chromosome are shown in pink and those aligned with the minus strand in violet (note that the direction of the reads was assigned arbitrarily, as sequencing was not oriented). Panel B: mapping of SL-containing reads. Panel C: previously annotated L. major genome (GeneDB database). Panel D: crude transcripts as assembled by Cufflinks. Panel E: new transcript annotation after mapping of both SL addition sites and the 3’ ends generated by polyadenylation. The images were generated after loading the RNA-seq data in the Integrative Genomics Viewer (IGV 2.1) .