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Old 10-04-2015, 09:20 PM   #1
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Location: Germany

Join Date: May 2010
Posts: 149
Default RNA-STAR filter out unique Junctions

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 * 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 file:

awk 'FNR==5442 {print}'
 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.

frymor is offline   Reply With Quote

splice junctions, star aligner

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