Understanding Exon Coordinates in MATS-output

[Tiago Bruno Castro]

Hello guys,

in the MATS-Output we got 6 columns with coordinates named:

[exonStart_0base] [exonEnd] [upstreamES] [upstreamEE] [downstreamES] [downstreamEE]

which I suppose are the coordinates of the 3 exons being avaliable in this example Exon Skipping.

I have some questions I could not find elsewhere.

1) Are all columns 0base based or just the first one?

2) The two columns are the coordinates of the skipped exon ? ( There is any reason for both columns not be in the middle? Between Upstream and Downstream exons)

3) EE means Exon End and ES means Exon Start?

4a) I note that some exons have different coordinates in 1, -1, -2 or 2 bases from the original gtf notation. Could this be explain or it is a bug (Figure 1) ?

4b) I could not find [exonStart_0base] [exonEnd] coordinates in the annotation ( the few I checked mannually)

Thank you for your patient.

[Tiago Bruno Castro]

Correction:

2) The first*** two columns are the coordinates of the skipped exon ? ( There is any reason for both columns not be in the middle? Between Upstream and Downstream exons)

[Shen Shihao]

1) Are all columns 0base based or just the first one?

All coordinates are 0 based.

2) The two columns are the coordinates of the skipped exon ? ( There is any reason for both columns not be in the middle? Between Upstream and Downstream exons)

The first two columns of coordinates are for the skipped exon.

3) EE means Exon End and ES means Exon Start?

Yes.

4a) I note that some exons have different coordinates in 1, -1, -2 or 2 bases from the original gtf notation. Could this be explain or it is a bug (Figure 1) ?

4b) I could not find [exonStart_0base] [exonEnd] coordinates in the annotation ( the few I checked mannually)

Could you tell us more about the annotation file you used? We will look into the issue if there is a difference. 

Thanks,

Shihao

[Tiago Bruno Castro]

I used Gencode, that is the same annotation of the ENSEMBL.