Header Leaderboard Ad

Collapse

RNA-STAR filter out unique Junctions

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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 *.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
    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:

    Code:
    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
Working...
X