questions about rMATS output

[zhaopei...@gmail.com]

Hi,

I am new to use rMATS for alternative splicing detection. I have a few questions:

1. i noticed that the default is no detection of novel splice sites (-novelSS 0). Why are there still files like 'fromGTF.novelEvents.A3SS.txt' in the ASEvents folder?

2. AS_Event.MATS.JunctionCountOnly.txt and AS_Event.MATS.ReadsOnTargetAndJunctionCounts.txt  generated different results. What are the advantages and disadvantages for these two types of files?

Thanks in advance.

[Shen Shihao]

1. i noticed that the default is no detection of novel splice sites (-novelSS 0). Why are there still files like 'fromGTF.novelEvents.A3SS.txt' in the ASEvents folder?

'fromGTF.novelEvents.A3SS.txt'  contains the novel alternative splicing events based on the known splice sites.

2. AS_Event.MATS.JunctionCountOnly.txt and AS_Event.MATS.ReadsOnTargetAndJunctionCounts.txt  generated different results. What are the advantages and disadvantages for these two types of files?

"AS_Event.MATS.JunctionCountOnly.txt" uses only junction read counts. 

"AS_Event.MATS.ReadsOnTargetAndJunctionCounts.txt" uses junction read counts + reads entirely on the target exon. 

Using both types of reads increases the statistical power, with the risk of getting more variation/bias from the mapping to exon body.

Thanks,

Shihao