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wurmlab / afra

Genome Annotation for the Masses
http://afra.sbcs.qmul.ac.uk
Apache License 2.0
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Ability to hide features that extend beyond a specified window #112

Open ilevantis opened 9 years ago

ilevantis commented 9 years ago

Would be incredibly helpful (especially with RNASeq / RNASeq Coverage) to hide all features in any(all) tracks that lie outside a specified window.

  1. This would be an easy way to get rid of mis-mapped RNASeq reads which have skips that are extremely long and span between genes.
  2. It would remove the visual clutter of other features that are obviously too long (therefore likely irrelevant) for what is being investigated.
  3. I imagine this could potentially improve performance when only investigating a small region.
yannickwurm commented 9 years ago

Are these weird RNASeq reads correctly or incorrectly mapped?

ilevantis commented 9 years ago

I don't have the actual RNASeq data to hand so I can't say for sure. I'm guessing that it might be due to 2 regions of very similar sequence being close together.

For example, a read that came from gene1 exon2-3, ends up mapped as spanning from gene1 exon2 to gene2 exon3 because gene1 exon3 and gene2 exon3 are very similar.

Have a look at the region Si_gnH.scaffold00008:424866..433120 for an example.