Hi everyone,
We are interested in discovering fusion genes in RNA-seq data from a
certain tumoral type, and FusionSeq seems to be a tool of choice for
this particular topic. Our RNA-seq data comes from the SOLID sequencing
platform, it is paired-end with 50bp-long reads on the 3' side and 25
bp-long reads on the 5' side.
Our main concern is the choice of the mapping strategy. We use Bfast+BWA, that has the advantage of being sensitive and capable of handling very short reads. Here is our mapping strategy : we aligned reads on the reference genome, then we extracted the non-aligned reads, and we aligned them on a library of all known human CDS. We then want to use FusionSeq for the search of fusion genes. As far as we understood FusionSeq takes as an input reads aligned on a genomic reference under the MRF format. Our concern here is the following : how to merge these two mappings (genome and CDS) into a single one, that we can then feed to FusionSeq ? Do we need to convert the coordinates of reads aligned on the CDS to genomic coordinates ? And if so, how ?
Thank you by advance for your help.
Jonas and Jaydutt
We are interested in discovering fusion genes in RNA-seq data from a
certain tumoral type, and FusionSeq seems to be a tool of choice for
this particular topic. Our RNA-seq data comes from the SOLID sequencing
platform, it is paired-end with 50bp-long reads on the 3' side and 25
bp-long reads on the 5' side.
Our main concern is the choice of the mapping strategy. We use Bfast+BWA, that has the advantage of being sensitive and capable of handling very short reads. Here is our mapping strategy : we aligned reads on the reference genome, then we extracted the non-aligned reads, and we aligned them on a library of all known human CDS. We then want to use FusionSeq for the search of fusion genes. As far as we understood FusionSeq takes as an input reads aligned on a genomic reference under the MRF format. Our concern here is the following : how to merge these two mappings (genome and CDS) into a single one, that we can then feed to FusionSeq ? Do we need to convert the coordinates of reads aligned on the CDS to genomic coordinates ? And if so, how ?
Thank you by advance for your help.
Jonas and Jaydutt
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