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Mobile Element finding crashes when contigs are identified across two IS elements #675

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dbgoodman opened this issue Jun 1, 2016 · 0 comments
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Mobile element calling code contains an assertion that both sets of vertices come from the same mobile element. We have found cases where this fails:

# in genome_finish/graph_contig_placement.py
>translocation_seq_verts
[ME_insertion_sequence:IS150_RC_121, ME_insertion_sequence:IS186_RC_253]

This could be because the mobile elements look similar at the alignment region.

There are two ways to fix this:

  1. ignore these mobile elements (not ideal)
  2. combine them with (IS150/IS186)

image

I think this is just a really confusing highly paralogous region. I blasted the contig and just got more confused. However, there is definitely an IS element involved here:

image

@dbgoodman dbgoodman added the bug label Jun 1, 2016
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