RNA seq data analysis by intron centric analysis gives insight about exon skkiping ,I have attached photo of excel file I have. Can anyone help me how to interpretate it
eg ENSMUSG00000039218:EENSMUSE00000995398_ENSMUSE00001055849
What is practical meaning of it ....and of p value
What is the software which is creating this output? These are Ensembl exon IDs for mouse, but how they are combined is not familiar to me. I would guess that the '+' and '_' symbols are indicating combinations and/or fusions of these exons, but it is impossible to know without knowing the software that created the output. Have you checked the user manual for a description of the output format?
In one publication (Nature immunology volume 16 number 4 april 2015) authors have done RNA seq after HuR knock out ,and aim was to to see valid exon skipping event,I was unable to interpret the file they provide.
Software was cited for Bioinformatics. 2013 Jan 15;29(2):273-4. doi: 10.1093/bioinformatics/bts678. Epub 2012 Nov 21.
Intron-centric estimation of alternative splicing from RNA-seq data.
Pervouchine DD1, Knowles DG, Guigó R.
The program that they used is called DexSeq. The output in the table that you provided appears to reference exons with the exon ID, and introns are represented with two exon IDs and an "_" between them. The introns do not have IDs in ensembl, and therefore are best referenced as the location between two exons. Therefore, "EENSMUSE00001224620+ENSMUSE00001278991+ENSMUSE00000691303_ENSMUSE00000656942" means the analysis refers to the sequence created by:
combining exons EENSMUSE00001224620 and ENSMUSE00001278991 and
the intron between exons ENSMUSE00000691303 and ENSMUSE00000656942.
Regarding the P-value, you should read the manual on the usage of DexSeq for that.
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