tophat v1.1.1 - "warning: multiple closures found for read"

[cs]

Hello all,
using tophat v1.1.1 x86_64 for paired-end (2-lanes) Illumina RNAseq
data, in the file "logs/long_spanning_reads.log" I see many messages
"warning: multiple closures found for read", using specified min-intron-length
and max-intron-length values. Is this something to be concerned about?
Do any parameters need to be adjusted?

Is this related to the bug-fix corrected in v1.1.2 released Oct 26 - "A sorting issue for pairs that align in multiple places has been fixed". Thanks.

[Daehwan]

Hello all,
using tophat v1.1.1 x86_64 for paired-end (2-lanes) Illumina RNAseq
data, in the file "logs/long_spanning_reads.log" I see many messages
"warning: multiple closures found for read", using specified min-intron-length
and max-intron-length values. Is this something to be concerned about?
Do any parameters need to be adjusted?

Is this related to the bug-fix corrected in v1.1.2 released Oct 26 - "A sorting issue for pairs that align in multiple places has been fixed". Thanks.

As you know, TopHat is a spliced read mapper, and for unmapped reads, TopHat tries to fill the gaps in them using user-provided or novel junctions (closures), but for some gaps, there seem to be more than one candidate junction for a gap where only one of them could be a true junction. TopHat, for such a case, doesn't fill the gaps.