RNA-STAR filter out unique Junctions

[frymor]

Hi all,

I am trying to filter un-annotated splice junction from my STAR mapping run, but with no success.
I would like to exclude all junction from both my *.bam and *.SJ.out.tab files which have less than 5 reads overlapping the junction motifs.
I have trid it several times with different parameters until I came these construction:

--alignSJoverhangMin 8
--alignSJDBoverhangMin 5
--outFilterType BySJout
--outSJfilterCountTotalMin 8 5 5 5
--outSJfilterCountUniqueMin -1 -1 -1 -1

With this settings I get a lot less junctions than with the default values. This is fine by me, as I hope only to get those with high coverage, but even here I still get this kind of junctions in my SJ.tab.out file:

awk 'FNR==5442 {print}' STAR.SJ.out.tab
 2L      11438179        11487284        1       1       0       1       0       22

This is an unannotated splice junction with only one read overlapping the intron motifs.

What do I need to change to get rid of these junctions as well?

Thanks in advance for the help.

Assa