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Old 10-05-2010, 09:58 PM   #1
ketan_bnf
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Default How to find fusion genes using bioinformatics, Need help?

Hi all,

I am new to this forum, actually i have 454 sequences and want to find fusion genes (chromosomal translocation) may be causing cancer, right now i am using BLAT, collecting sequences having min. 100bp alignment and above 93% identity.

1) Is there any tool or pipeline that directly predict fusion genes?

2) Is there any perl script to extract result from BLAT output using my parameters?

3) Am i going in right way?

Regards.
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Old 10-06-2010, 09:34 PM   #2
malachig
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Is your data from genomic DNA or RNA? There are probably others, but here are some possibilities off the top:

DeFuse, BreakDancer, Trans-ABySS, NextGENe, some relevant papers here and here, and here.

We have used DeFuse successfully at our center so that would be my first recommendation if you have RNA-seq data...
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Old 10-07-2010, 09:42 PM   #3
ketan_bnf
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Thanks for your reply.


My data is a transcriptome data. I didn't know about BFAST and SAM tools, i'll try it and confirm whether it's apporproate for my data.


Regards,
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Old 12-02-2010, 02:24 PM   #4
townway
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would you share some your experience of defuse?

when I modified config.txt like
# Directory where you have decompressed your dataset
dataset_dir = /gs1/users/defuse-0.3.3/
dataset_prefix = /gs1/users/defuse-0.3.3/Homo_sapiens.GRCh37.59

it always showed the error "does not exist the file /gs1/users/tangwei/defuse-0.3.3/Homo_sapiens.GRCh37.59"


Thank you

Wei


Quote:
Originally Posted by malachig View Post
Is your data from genomic DNA or RNA? There are probably others, but here are some possibilities off the top:

DeFuse, BreakDancer, Trans-ABySS, NextGENe, some relevant papers here and here, and here.

We have used DeFuse successfully at our center so that would be my first recommendation if you have RNA-seq data...
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Old 12-16-2010, 08:30 PM   #5
andrewm
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Do you have a space after Homo_sapiens.GRCh37.59
If you would like to email me the config file directly, i can take a look.

Andrew

amcphers
at
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Old 12-17-2010, 11:59 AM   #6
townway
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Thank you Andrew.
The main problem for me as you said is the text editor messing everything up.
now it is running.


Quote:
Originally Posted by andrewm View Post
Do you have a space after Homo_sapiens.GRCh37.59
If you would like to email me the config file directly, i can take a look.

Andrew

amcphers
at
bccrc
dot
ca
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Old 05-10-2011, 09:25 PM   #7
Brajbio
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Did some one has worked on FusionSeq or FusionHunter. How are these tools comparatively with DeFuse in terms of performance and usability???
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Old 05-10-2011, 09:35 PM   #8
Brajbio
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can tophat be used for detection of gene fusion?
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Old 05-11-2011, 03:16 AM   #9
jochensupper
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Brajbio,

most gene fusion tools use paired-end information to detect gene fusion candidates. So in principle you could map with tophat but depending on your downstream gene fusion detection tool, the "split" alignments might not be taken into account. Some tools, however, re-align reads to the detected breakpoint region to determine the exact breakpoint.

Quote:
Originally Posted by Brajbio View Post
can tophat be used for detection of gene fusion?
We (Genomatix) have a gene fusion detection tool that will use "split" reads to detect gene fusion candidates.
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Old 06-27-2011, 04:23 AM   #10
kissthefuture
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Quote:
Originally Posted by townway View Post
would you share some your experience of defuse?

when I modified config.txt like
# Directory where you have decompressed your dataset
dataset_dir = /gs1/users/defuse-0.3.3/
dataset_prefix = /gs1/users/defuse-0.3.3/Homo_sapiens.GRCh37.59

it always showed the error "does not exist the file /gs1/users/tangwei/defuse-0.3.3/Homo_sapiens.GRCh37.59"


Thank you

Wei
hi, I find that your defuse version is so old.Please use 0.3.6 or 0.6.2
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Old 06-27-2011, 04:13 PM   #11
malachig
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I would also suggest you update to 0.4.2. The way these things are specified in the config file have changed slightly. The new example may be more clear. After you have tried that, if you are still having difficulty, email your config file to the author or post it here and we can take a look....
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Old 06-28-2011, 04:06 AM   #12
GenoMax
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Mapsplice may also be an option you can try: http://www.netlab.uky.edu/p/bioinfo/MapSplice
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Old 09-29-2011, 01:20 AM   #13
srividya
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Default deFuse error.

Hello,

I am trying to use defuse. I tried to create the 2bit reference genome file. I got some errors. Can anyone check if there is some mistake with the config file that i changed?

/Apps/serial/defuse/defuse-0.4.3/scripts/create_reference_dataset.pl -c config.txt

This is the error that I got when I ran the create_reference_dataset.pl,

Use of uninitialized value in concatenation (.) or string at /Apps/serial/defuse/defuse-0.4.3/scripts/cmdrunner.pm line 39.

Thanks,
Srividya
Attached Files
File Type: txt config.txt (7.6 KB, 40 views)
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Old 09-30-2011, 12:41 PM   #14
andrewm
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Your config.txt appears to be fine. However, the perl function abs_path is returning null. What operating system are you using? And which version of perl?

If you want, you can reach me quicker by email at the address listed on this page:
http://defuse.sourceforge.net

Quote:
Originally Posted by srividya View Post
Hello,

I am trying to use defuse. I tried to create the 2bit reference genome file. I got some errors. Can anyone check if there is some mistake with the config file that i changed?

/Apps/serial/defuse/defuse-0.4.3/scripts/create_reference_dataset.pl -c config.txt

This is the error that I got when I ran the create_reference_dataset.pl,

Use of uninitialized value in concatenation (.) or string at /Apps/serial/defuse/defuse-0.4.3/scripts/cmdrunner.pm line 39.

Thanks,
Srividya
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Old 10-01-2011, 05:13 PM   #15
mjn138
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Default FusionMap

You may also try out FusionMap, from Omicsoft. http://omicsoft.com/fusionmap/

It works with single end reads as well. The paper is at http://bioinformatics.oxfordjournals...tr310.abstract

It runs on both windows and linux.
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Old 02-22-2012, 04:16 AM   #16
salzberg
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Quote:
Originally Posted by Brajbio View Post
can tophat be used for detection of gene fusion?
Several people asked about TopHat. Since last summer (2011), we have released TopHat-Fusion, which can detect fusion transcripts from either single reads or paired end reads. It is very fast and highly effective at filtering out the numerous false positives that plague these types of tools.
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Old 02-22-2012, 07:46 AM   #17
Dameon
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I recommend MapSplice for detecting gene fusions in PE data. I use the full-running, cluster, MapPer, and filter-fusion-by-repeat options. I like how it reports putative gene fusions in an easily annotated bed file.
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Old 02-22-2012, 08:37 AM   #18
Nicolas
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Quote:
Originally Posted by salzberg View Post
Several people asked about TopHat. Since last summer (2011), we have released TopHat-Fusion, which can detect fusion transcripts from either single reads or paired end reads. It is very fast and highly effective at filtering out the numerous false positives that plague these types of tools.
Hi,
I am sure Tophat-fusion is awesome, but it would be great to get some feedback on the problems observed by several users and reported here :

http://seqanswers.com/forums/showthread.php?t=12953

Thanks,

Nicolas
PS: I've sent an email to tophat.cufflinks@gmail.com but with no success....
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Old 02-22-2012, 08:38 AM   #19
salzberg
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Also I forgot to mention that TopHat-Fusion can handle SOLiD reads (as can TopHat).
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Old 03-19-2012, 02:26 AM   #20
JMath
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Default Problems with running DeFuse

Problem solved

Last edited by JMath; 03-21-2012 at 01:36 AM.
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