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Stranded Paired-end RNA-seq coloring and wig/bw support

asked 2017-10-24 08:19:14 -0700

Michael Imbeault gravatar image

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.

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answered 2017-11-09 15:34:26 -0700

Hey Michael,

Thanks for the feature suggestions. The "first in strand" coloring sounds interesting and I see why it would be a helpful way to visualize reads. I have created a ticket to capture that coloring mode. We are not actively adding features to GB currently, but may in the future have a GB feature push.

We looked into bigwig support and even had an experimental version working. Unfortunately it's a pretty funky binary file format from the UCSC guys and we had a number of issues with it. We will revisit this at some point as well.

WIG files are actually supported by GB. You need to "convert" them first. Just select them in the Convert wizard (from the data manager or Plot window).

Thanks, Gabe

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Also, UCSC offers some tools to make the conversions between these formats. http://genome.ucsc.edu/goldenpath/help/bigWig.html

SteveHystad ( 2017-11-09 15:36:49 -0700 )edit

Thanks for the answer - didn't know about wig support, that is at least something, even if the files are huge and the conversion process takes time. Hopefully other features can be added in at a later time, the interface of GenomeBrowse is so much superior to other options!

Michael Imbeault ( 2017-11-10 06:34:47 -0700 )edit
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Asked: 2017-10-24 08:19:14 -0700

Seen: 13 times

Last updated: Nov 09