SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Newsbot! Literature Watch 5 07-13-2013 01:02 AM
tophat-fusion error ptong7 Bioinformatics 9 11-03-2012 03:00 AM
errors of tophat fusion jiexiong Bioinformatics 12 03-22-2012 03:43 AM
tophat fusion --fusion-min-dist MerFer Bioinformatics 1 07-24-2011 08:09 PM
tophat fusion MerFer Bioinformatics 0 06-15-2011 01:31 AM

Reply
 
Thread Tools
Old 09-18-2011, 10:24 PM   #1
jaycekoh
Junior Member
 
Location: sg

Join Date: Sep 2011
Posts: 2
Default queries about tophat fusion output

I have some queries about result.html, http://tophat-fusion.sourceforge.net/data/result.html, explanations of which I do not understand

9. Number of spanning mate pairs
10. Number of spanning mate pairs where one end spans a fusion
11. If you follow the the 9th column, it shows coordinates "number1:number2" where one end is located at a distance of "number1" bases from the left genomic coordinate of a fusion and "number2" is similarly defined

Am I right to say that 9. represents the number of paired ends, with one end totally on one chromosome of a fusion, and the other totally on the other chromosome of a fusion?

Would I also be right to say that 10. is the same as 9., except that 9. has no end spanning a fusion, and 10. has one end spanning. Which is to say that 9. and 10. are mutually exclusive.

Given the above definitions, from the eg in result.html

4. chr20-chr20 rf

MCF7
SULF2
chr20
46415145
ENSG00000171940
chr20
52210297
22
18
27

MCF7
SULF2
chr20
46415146
ENSG00000171940
chr20
52210647
11
18
14

22 sets the limit on the number of reads spanning a fusion, why is the number 27 greater than 22?

For 11. is it possible to give an illustration of what exactly you mean? I did the math by adding the genomic coordinate to the number and compared it to the coordinates in the reads section but the numbers do not match up. Also what is the difference between and + number1 and number2

Really grateful if you can enlighten me!
i have tried looking at the documentation but it is cryptic. i hope i am not sounding just at cryptic trying to put across concepts that require illustration.
jaycekoh is offline   Reply With Quote
Old 12-20-2012, 01:25 AM   #2
mxqian
Junior Member
 
Location: shanghai

Join Date: Sep 2011
Posts: 3
Default

I also want to get the answer!!!
mxqian is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:17 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO