8000 Option for circular genome alignment and counting · Issue #54 · formbio/laava · GitHub
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Option for circular genome alignment and counting #54

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etal opened this issue Aug 15, 2024 · 0 comments
Open

Option for circular genome alignment and counting #54

etal opened this issue Aug 15, 2024 · 0 comments

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@etal
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etal commented Aug 15, 2024

If the vector plasmid is circular, but the reference sequence is linear, sequencing reads spanning the origin will appear in the SAM/BAM output with two alignments, one on each side of the origin, and a misleading two-part classification such as "backbone|vector+backbone".

Add a workflow input option for whether the vector reference should be treated as circular (boolean). Then, if circular:

  • Perform read mapping twice -- once with the linear reference as-is, and again with the full reference sequence concatenated end-to-end.
  • Then, resolve reads spanning the origin in the concatenated reference versus the corresponding reads in the original linear reference. Ensure that the same total number of reads are present in the output, i.e. no reads are duplicated or lost after resolution. Consider adding the "TP" tag to the output BAM header and allowing read coordinates to go beyond the reference end -- see SAM/BAM support for circular reference sequences.
  • Classify origin-spanning reads (primarily backbone and vector+backbone) using modular arithmetic so that the alignment coordinates used in the report stay within the original reference's boundaries.
@etal etal added this to the v3.2 milestone Aug 15, 2024
@etal etal modified the milestones: v3.2, v3.x Nov 22, 2024
@etal etal removed this from the v3.x milestone Mar 10, 2025
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