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Hi,
This is a difficult question and specific to MATS, but if there is anyone familiar with MATS, I would be grateful for the help.
I've already emailed the authors, but I haven't yet received an answer.
I've been running MATS to identify differentially spliced exons.
Overall, I'm satisfied with the results. I've confirmed with IGV some of the differentially spliced exons.
However, MATS missed a few differentially spliced exons in the Macf1 gene that to me are quite evident to me in IGV.
The annotation file used was the most recent (version 77) Ensembl GTF file for M. musculus.
I've put in attachment an IGV screenshot, and a Sashimi plot generated with IGV, of the differentially spliced exons that MATS did not identify.
I also grepped Macf1 in the folder ASEvent, which is supposed to contain all possible alternative splicing events, and none of the exons returned correspond to the differentially spliced exons identified with IGV.
So, it appears MATS did not even test for these exons.
Could this be a parsing problem of the Ensembl GTF file?
The differentially spliced exons do appear in the GTF file, as illustrated both in the IGV screenshots and the text file in attachment with the grep results for Macf1 on the Ensembl GTF file.
Thank you for your help.
This is a difficult question and specific to MATS, but if there is anyone familiar with MATS, I would be grateful for the help.
I've already emailed the authors, but I haven't yet received an answer.
I've been running MATS to identify differentially spliced exons.
Overall, I'm satisfied with the results. I've confirmed with IGV some of the differentially spliced exons.
However, MATS missed a few differentially spliced exons in the Macf1 gene that to me are quite evident to me in IGV.
The annotation file used was the most recent (version 77) Ensembl GTF file for M. musculus.
I've put in attachment an IGV screenshot, and a Sashimi plot generated with IGV, of the differentially spliced exons that MATS did not identify.
I also grepped Macf1 in the folder ASEvent, which is supposed to contain all possible alternative splicing events, and none of the exons returned correspond to the differentially spliced exons identified with IGV.
So, it appears MATS did not even test for these exons.
Could this be a parsing problem of the Ensembl GTF file?
The differentially spliced exons do appear in the GTF file, as illustrated both in the IGV screenshots and the text file in attachment with the grep results for Macf1 on the Ensembl GTF file.
Code:
[username@lg-1r17-n04 ASEvents]$ basename `pwd` ASEvents [username@lg-1r17-n04 ASEvents]$ grep Macf1 * fromGTF.A3SS.txt:1289 "ENSMUSG00000028649" "Macf1" 4 - 123368820 123368835 123368820 123368832 123369804 123369968 fromGTF.A5SS.txt:799 "ENSMUSG00000028649" "Macf1" 4 - 123438466 123438666 123438472 123438666 123434699 123435195 fromGTF.AFE.txt:5765 "ENSMUSG00000028649" "Macf1" 4 - 123683969 123684360 123564462 123564694 123554303 123554365 fromGTF.AFE.txt:5766 "ENSMUSG00000028649" "Macf1" 4 - 123664465 123664752 123564462 123564694 123554303 123554365 fromGTF.AFE.txt:5767 "ENSMUSG00000028649" "Macf1" 4 - 123683969 123684360 123664465 123664752 123554303 123554365 fromGTF.SE.txt:5013 "ENSMUSG00000028649" "Macf1" 4 - 123364056 123364074 123360909 123361027 123365272 123365347 fromGTF.SE.txt:5014 "ENSMUSG00000028649" "Macf1" 4 - 123397093 123397420 123395912 123395997 123397747 123397907 fromGTF.SE.txt:5015 "ENSMUSG00000028649" "Macf1" 4 - 123354478 123354580 123351821 123351951 123355055 123355267 fromGTF.SE.txt:5016 "ENSMUSG00000028649" "Macf1" 4 - 123441602 123441665 123440549 123440791 123444834 123444952 fromGTF.SE.txt:5017 "ENSMUSG00000028649" "Macf1" 4 - 123368820 123368832 123367874 123368037 123369804 123369968 fromGTF.SE.txt:5018 "ENSMUSG00000028649" "Macf1" 4 - 123368820 123368835 123367874 123368037 123369804 123369968 fromGTF.SE.txt:5019 "ENSMUSG00000028649" "Macf1" 4 - 123386548 123386557 123385454 123385686 123387227 123387431
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