#1337 closed defect (fixed)
Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v4.33 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description (last modified by )
This was initially thought to be a problem with an incorrect value for the --mate-inner-dist parameter due to lot of clipping when sequencing 2x150 reads (see #1336 and #1335).
However, investigations shows that there is a bug in Tophat when marking aligned pairs as a proper pairs that is triggered when the --mate-inner-dist parameter is negative and --mate-std-dev is less than abs(--mate-inner-dist). For example:
--mate-inner-dist -80 --mate-std-dev 79 // will trigger the bug --mate-inner-dist -79 --mate-std-dev 79 // works
To avoid triggering the bug we should make sure that the --mate-inner-dist parameter always is large enough.
Attachments (1)
Change History (4)
comment:1 by , 3 years ago
| Description: | modified (diff) |
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by , 3 years ago
| Attachment: | tophat-alignedpairs-vs-innerdist.png added |
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comment:2 by , 3 years ago
| Resolution: | → fixed |
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| Status: | new → closed |
comment:3 by , 3 years ago
This bug may also be related to #1325. The same bug is also present in Tophat.
It seems like the "proper pair" flag is incorrect only for those alignments where both reads have a negative distance.
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