Does "fromGTF.[AS type].txt" include all events in "fromGTF.novelEvents.[AS type].txt" ?

[Yaoi T]

Hello,

 I got the results of rMATS-3.2.5 and try comparing the novel AS exons and sites berween two groups.

For the object, I first looked into  "fromGTF.[AS type].txt" and "fromGTF.novelEvents.[AS type].txt" in ASevents folder.

Using the command ' wc -l ', I got the number of lines in each.

For example,

43960 fromGTF.SE.txt

32427 fromGTF.novelEvents.SE.txt

In the past thread, the comment was posted that "fromGTF.SE.txt" was created from GTF file.

Though I believed "fromGTF.SE.txt" includes  known AS events alone, I found many common AS events between both files.

So, it looks like that  "fromGTF.SE.txt" include all events in "fromGTF.novelEvents.SE.txt": ca. 12000 known AS events and ca.32500 novel ones. 

Is it right that  "fromGTF.[AS type].txt" include all events in "fromGTF.novelEvents.[AS type].txt" ?

Moreover, does the novel events in the GTF include experimental artifacts ?

Thanks,

Yaoi T

[Juw Won Park]

Hello,

Yes, as you pointed out, the novelEvents.txt are subset of the other file. 

Some novel events could be from inherited artifacts (sequencing error, base calling error, etc.). However, the novel events from those errors will have a small number of reads thus they will highly likely to be reported as non-significant. 

-Juw Won

[Gmail]

Hello, Juw Won

I have one more question:

Is the same unique IDs in both files defined as the common ones? 

If so, I can easily extracted the known events from "fromGTF.[AS type].txt" file.

Thanks,

Yaoi T

2016/09/24 6:29、Juw Won Park <rmat...@gmail.com> のメール：

-- 
You received this message because you are subscribed to the Google Groups "rMATS User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rmats-user-gro...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/rmats-user-group/8dd4df88-eb1f-47cc-9148-df12b785a674%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Juw Won Park]

Yes, exactly!

-Juw Won

To unsubscribe from this group and stop receiving emails from it, send an email to rmats-user-group+unsub...@googlegroups.com.

[Yaoi T]

Thanks for your little efforts to enhance usability, Juw Won !

Yaoi T

2016年10月4日火曜日 1時27分51秒 UTC+9 Juw Won Park: