The read mapping data can be created by any mapping tool generating SAM or BAM files (Li et al., 2009), like bwa (Li and Durbin, 2009), or with SARUMAN (Blom et al., 2011), generating JOK output files.
For the generation of static pathway map images, users should use the mapping tool to generate a custom pathway map, and download this image to make permanent modifications.
We chose TopHat v1.4.0 to align paired-end clean reads to the reference genome, because this mapping tool can generate a database of splice junctions based on the gene model annotation file, thus producing a better mapping result than other non-splice mapping tools [ 31, 69].
After the mapping is done, this tool generates a web archive (war) file, which can be deployed as web service and publishes data via Web Feature Service.
We used TopHat2 as the mapping tool because it can generate a database of splice junctions based on Ensemble annotations of galGal4 and thus can produce a better mapping result than other non-splice mapping tools.
TopHat was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file and thus give a better mapping result than other non-splice mapping tools.
The base map of the left panel was generated with the Generic Mapping Tools (GMT) map generator (http://woodshole.er.usgs.gov/mapit/).gov/mapit/
