Stranded Paired-end RNA-seq coloring and wig/bw support
Hello,
GenomeBrowse is by far my favorite genome browser, but it has a two shortcomings that prevent me from using it from everything (and recommending it to everyone I know).
One issue is the visualization of stranded, paired end RNA-seq - in IGV you have the option to color by 'first in strand', so that the mate pairs both have the same color, which allow you to visualize strand specificity for reads. Right now in GenomeBrowse it colors both mates separately, and with Illumina since they both are on different strands, you get a mix of forward and reverse-colored reads no matter the actual strandness of the pair.
Second issue is no wig or bigwig support, which prevents the import of most publicly available tracks (say from UCSC) without downloading the FASTQ and remapping to BAM. GenomeBrowse lacking this feature is somewhat puzzling, as these file formats are straightforward (at least compared to BAM) and very similar to coverage plots that it produces itself from BAM files.
Now I understand that both these use cases are not directly linked to other products in the suite of Golden Helix, but they would make GenomeBrowse usable for all common analysis scenarios. Please consider the implementation of both these features.
