Question: 5', 3' SS and Intron retention read count using STAR out.tab
0
gravatar for thindmarsmission
6 months ago by
thindmarsmission0 wrote:

Hi!

I am interested in the study of alternative splicing sites 5 and 3 and Intron retenton. I just want it, in the form of read count that how many numbers of reads and percentage of reads/total coverage reads, belongs to one splice site and same thing for other site.

NOTE: I don't have two different conditions.(so i am not considering MATS and related tools)

I aligned reads to reference using STAR and I have STAR out.tab file with unannotated and annotated events. Now, How I can extract information like listed below for 5',3' SS and IR events.

example [5' SS]:

                 start                    end                      number_of_reads
  chr1            10300                10500                      40
  chr1            10350                10500                       150
ADD COMMENTlink modified 6 months ago • written 6 months ago by thindmarsmission0
3

You might be interested in tools like SGSeq: https://bioconductor.org/packages/release/bioc/html/SGSeq.html

It reads from the aligned bam. It isn't the fastest tool, but from personal experience, it's pretty sensitive for both annotated and novel events.

Note: 3'ss and 5'ss stand for 3' splice site and 5' splice site, respectively. AS stands for alternative splicing. People in the field don't use ASS an acronym.

ADD REPLYlink modified 6 months ago • written 6 months ago by Eric Lim1.3k

Thanks for suggestion. I am just trying out this tool. Do you think, I can find Intron retention events using this tool?

ADD REPLYlink written 6 months ago by thindmarsmission0

Yes, my best understanding is that most tools rely on annotated exons to call intron retention (IR). Some tools infer IR by accessing exon-intron junction reads at both 5'ss and 3'ss. This approach is generally correct but will produce some false positives on those introns when both splice sites are alternatively spliced.

ADD REPLYlink written 6 months ago by Eric Lim1.3k

No: based on my reading of the paper and skimming the source code, it appears to me that SGSeq does not analyze IR.

ADD REPLYlink written 4 weeks ago by Malcolm.Cook1.0k
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