Gene Fusion Annotation pipeline

fabate · 02-13-2013, 02:25 PM

Hi everybody!

I'm pleased to announce Pegasus, a pipeline for the annotation of gene fusions. The tool is built on top of fusion detection tools (defuse and chimerascan are the supported one, but we are working to extend it) and it allows to assembly fusion sequence, both of nucleotides and amino acids, and annotate the lost and conserved protein domains.

The tool is still under development as well the documentation, but it is available at:

http://sourceforge.net/projects/pegasus-fus/

I applied this tool to many analysis and I found very useful to focus on biologically relevant fusions. So I decided to share it!

Contact me for any question! I hope you like it!

ndaniel · 02-13-2013, 11:53 PM

Quote:

Originally Posted by fabate

Hi everybody!

I'm pleased to announce Pegasus, a pipeline for the annotation of gene fusions. The tool is built on top of fusion detection tools (defuse and chimerascan are the supported one, but we are working to extend it) and it allows to assembly fusion sequence, both of nucleotides and amino acids, and annotate the lost and conserved protein domains.

The tool is still under development as well the documentation, but it is available at:

http://sourceforge.net/projects/pegasus-fus/

I applied this tool to many analysis and I found very useful to focus on biologically relevant fusions. So I decided to share it!

Contact me for any question! I hope you like it!

Does it work with FusionCatcher <http://code.google.com/p/fusioncatcher/> ?

Charitra · 03-25-2013, 05:37 PM

thank you for givin pipeline

may I ask you if you have any idea about tophat2-fusion vs defuse vs your one.

I have differences in my results obtained from Tophat2-Fusion vs defuse. There is single matching fusion gene between tophat and deFuse in one cell line. remaining 4 cell lines, there is none. n=5

tutorial commands, which I also used, are:
tophat2Fusion
tophat -o tophat_Calu-3 -p 8 --fusion-search --keep-fasta-order --bowtie 1 --no-coverage-search -r 0 --mate-std-dev 80 --max-intron-length 100000 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /data/tmkim/Tools/bowtie-0.12.9/hg19 Calu-3RNA_1.fastq Calu-3RNA_2.fastq

Post Fusion
tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /data/tmkim/Tools/bowtie-0.12.9/hg19

do you think your pipeline will be best for fusion.

Thank you.

fabate · 04-03-2013, 11:35 AM

Hi Charitra,

actually Pegasus is a fusion annotation system that runs on top of fusion detection tools like deFuse and Tophat2-fusion. So you can provide for example defuse output and it will create fusion transcript annotations that will help to select those fusions that best fit some cancer related features.

Currently it still does not support tophat2-fusion, but it support defuse. if you can create a defuse-like report file of tophat2-fusion report you will be able to run it.

Hope it helps.

fabate · 04-03-2013, 11:36 AM

Hi ndaniel,

currently FusionCatcher is not yet supported. We will work on that in the feature.

Charitra · 04-03-2013, 05:19 PM

Thank Dr Fabate

defuse-like report file of tophat2 fusion? I hope it means data parsing of tophat2fusion and producing deFuse like format , and providing to fusion catcher.

However, I have tophat-postfusions n=17...

fabate · 04-04-2013, 06:47 AM

I mean exactly that. It's just a matter of formatting the report.

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02-13-2013, 02:25 PM	#1
fabate Junior Member Location: New York Join Date: Feb 2013 Posts: 4	Gene Fusion Annotation pipeline Hi everybody! I'm pleased to announce Pegasus, a pipeline for the annotation of gene fusions. The tool is built on top of fusion detection tools (defuse and chimerascan are the supported one, but we are working to extend it) and it allows to assembly fusion sequence, both of nucleotides and amino acids, and annotate the lost and conserved protein domains. The tool is still under development as well the documentation, but it is available at: http://sourceforge.net/projects/pegasus-fus/ I applied this tool to many analysis and I found very useful to focus on biologically relevant fusions. So I decided to share it! Contact me for any question! I hope you like it!

03-25-2013, 05:37 PM	#3
Charitra Member Location: Seoul, Korea Join Date: Feb 2013 Posts: 57	Gene Fusion Annotation pipeline thank you for givin pipeline may I ask you if you have any idea about tophat2-fusion vs defuse vs your one. I have differences in my results obtained from Tophat2-Fusion vs defuse. There is single matching fusion gene between tophat and deFuse in one cell line. remaining 4 cell lines, there is none. n=5 tutorial commands, which I also used, are: tophat2Fusion tophat -o tophat_Calu-3 -p 8 --fusion-search --keep-fasta-order --bowtie 1 --no-coverage-search -r 0 --mate-std-dev 80 --max-intron-length 100000 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /data/tmkim/Tools/bowtie-0.12.9/hg19 Calu-3RNA_1.fastq Calu-3RNA_2.fastq Post Fusion tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /data/tmkim/Tools/bowtie-0.12.9/hg19 do you think your pipeline will be best for fusion. Thank you.

04-03-2013, 11:35 AM	#4
fabate Junior Member Location: New York Join Date: Feb 2013 Posts: 4	Hi Charitra, actually Pegasus is a fusion annotation system that runs on top of fusion detection tools like deFuse and Tophat2-fusion. So you can provide for example defuse output and it will create fusion transcript annotations that will help to select those fusions that best fit some cancer related features. Currently it still does not support tophat2-fusion, but it support defuse. if you can create a defuse-like report file of tophat2-fusion report you will be able to run it. Hope it helps.

04-03-2013, 11:36 AM	#5
fabate Junior Member Location: New York Join Date: Feb 2013 Posts: 4	Hi ndaniel, currently FusionCatcher is not yet supported. We will work on that in the feature.

04-03-2013, 05:19 PM	#6
Charitra Member Location: Seoul, Korea Join Date: Feb 2013 Posts: 57	Thank Dr Fabate defuse-like report file of tophat2 fusion? I hope it means data parsing of tophat2fusion and producing deFuse like format , and providing to fusion catcher. However, I have tophat-postfusions n=17...

04-04-2013, 06:47 AM	#7
fabate Junior Member Location: New York Join Date: Feb 2013 Posts: 4	I mean exactly that. It's just a matter of formatting the report.