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bioviz.bsky.social
BioViz
@bioviz.bsky.social
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Open source genome visualization for everyone featuring the Integrated Genome Browser, free for all from BioViz.org.
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bioviz.bsky.social
Deepthi made a cool new App! It's an IGB track filter. It hides alignments of sequence reads that contain really big gaps, an artifact (usually) from running RNA-to-genome alignment algorithms without setting a maximum intron size parameter. apps.bioviz.org/apps/reads-w...
This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left. This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left.
June 27, 2025 at 5:35 PM
bioviz.bsky.social
Here's an image showing two tracks of single-cell RNA-Seq data from tomato aligned using STARsolo. One track shows what happens when you don't set the maximum intron parameter. The result: Lots of alignments that are way, way, way too big! Our advice: Always view your alignments in a genome browser.
An image from Integrated Genome Browser showing two tracks. Both tracks contain data from SRA accession SRR30982326 aligned using STARsolo at UseGalaxy.eu. The parameters used for each track were the same, except that the top track specified parameter --alignIntronMax 5000. The vertical zoom is set so that you can see all alignments in the region are visible. There are thousands, and so each individual alignment looks like a thin horizontal line in this view. Hopefully, you can see that when we use the default maximum intron size, many apparently spurious alignments get created that extend far outside the gene shown in the gene models track. However, in the top track, it looks like there may be another gene upstream of the gene that is shown. We've seen this type of thing many times in the past with plant genomes. Plant genomes generally have very small introns (compared to mammals) and often have multiple duplicated genes side-by-side on the same chromosome. This makes alignments -- and assemblies! -- difficult sometimes.
June 11, 2025 at 6:37 PM