Question: How to validate translocation detected in RNA-seq data?
2
gravatar for alisaber814
5.4 years ago by
alisaber81420
Netherlands
alisaber81420 wrote:

Hi everyone,

Recently, we performed paired end RNA-seq. and last week I got detected translocation list from our bioinformatician. In the file that I have there are both genes involved in the fusion transcript and also number of split and span reads and sequence of the fusion (almost 150 bp from each side). Now, I am trying to BLAT this sequences, make pictures for each fusion gene, design the primer and sequence them for validation. But, I have some problems with some of the fusions. In some of the cases I have complementary sequence of gene A fused with correct sequence of gene B (both genes in the same direction in the chromosome). How can this happen? Is it because of inversion (in the report, indicated that there is no inversion)? How should I design the primers; should I used reference genome for primer design or the sequence that I have from RNA-seq? Thank you very much.

Ali

sequencing rna-seq next-gen • 2.5k views
ADD COMMENTlink modified 5.4 years ago by emissrto10 • written 5.4 years ago by alisaber81420
1
gravatar for emissrto
5.4 years ago by
emissrto10
emissrto10 wrote:

could it be two isoforms or variants unspecified Refseq RNA# artifact with specific DNAs results. (The fusion molecules could supress or inhibit DNA assay or reassembly) refer to: Similar posts if you have (at least >100 bp ..Ngs Data V.S Microarray Data) somebody might have tried this before.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by emissrto10

Also I would think it would be an allel Api Variation Tools And 1000Genomes Dbsnp132 (comment) with undefined exon or intron which has a (tag) efetch not in the currently usage in use in the human reference assembly

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by emissrto10
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