Entering edit mode
6.0 years ago
Gabby
▴
20
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
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.
Thanks for suggestion. I am just trying out this tool. Do you think, I can find Intron retention events using this tool?
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.
No: based on my reading of the paper and skimming the source code, it appears to me that SGSeq does not analyze IR.