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:
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:
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
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:
Code:
--alignSJoverhangMin 8 --alignSJDBoverhangMin 5 --outFilterType BySJout --outSJfilterCountTotalMin 8 5 5 5 --outSJfilterCountUniqueMin -1 -1 -1 -1
Code:
awk 'FNR==5442 {print}' STAR.SJ.out.tab 2L 11438179 11487284 1 1 0 1 0 22
What do I need to change to get rid of these junctions as well?
Thanks in advance for the help.
Assa