Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#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:

Description (last modified by Nicklas Nordborg)

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)

tophat-alignedpairs-vs-innerdist.png (20.6 KB ) - added by Nicklas Nordborg 3 years ago.

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Change History (4)

comment:1 by Nicklas Nordborg, 3 years ago

Description: modified (diff)

by Nicklas Nordborg, 3 years ago

comment:2 by Nicklas Nordborg, 3 years ago

Resolution: fixed
Status: newclosed

In 6423:

Fixes #1337: Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0

comment:3 by Nicklas Nordborg, 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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