Fusion Hunter for Finding Fusion genes

[alvarani]

Hi All ,

I am using Fusion Hunter for finding Fusion transcripts from RNA-seq data. Mine is Paired end datasets. Which is not alike to left and Right ends, but when I give it in the command line with FusionHunter

I am getting the following Error message,
Unexpected parameterTue Apr 1 18:53:31 2014: Checking configurations
You should check your configuration file, L read should not be the same as R read!

The command I used,

${fusionH}/FusionHunter.pl FusionHunter.cfg L=/home/USER/Rna_seq_patient_1/RE_3_L001_1.fastq; R=/home/USER/Rna_seq_patient_1/RE_3_L001_2.fastq; BowtieIdx=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/bowtie_index/hg19 Gene_annotation=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/hg19.ucscKnownGene

It would be great if soemone could help me to knwo where I am going wrong.

I have checked both Left and right reads which is not SAME

Thank you

[ndaniel]

Hi All ,

I am using Fusion Hunter for finding Fusion transcripts from RNA-seq data. Mine is Paired end datasets. Which is not alike to left and Right ends, but when I give it in the command line with FusionHunter

I am getting the following Error message,
Unexpected parameterTue Apr 1 18:53:31 2014: Checking configurations
You should check your configuration file, L read should not be the same as R read!

The command I used,

${fusionH}/FusionHunter.pl FusionHunter.cfg L=/home/USER/Rna_seq_patient_1/RE_3_L001_1.fastq; R=/home/USER/Rna_seq_patient_1/RE_3_L001_2.fastq; BowtieIdx=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/bowtie_index/hg19 Gene_annotation=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/hg19.ucscKnownGene

It would be great if soemone could help me to knwo where I am going wrong.

I have checked both Left and right reads which is not SAME

Thank you

Have you tried FusionCatcher?

http://code.google.com/p/fusioncatcher/

[alvarani]

Thanks I have tried and its working perfectly..

[[email protected]]

Is there any way to avoid this problem in Fusion hunter? I want to compare several tools.

Have you tried FusionCatcher?
http://code.google.com/p/fusioncatcher/