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suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
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How to get the position of the fused gene on the chromosome? #198

Closed wiltbb closed 1 year ago

wiltbb commented 1 year ago

I would like to know where the fused genes are located for GWAS analysis, but I am finding it difficult to determine the exact location of the fused genes on the chromosomes.Do you have a good method? Thank you in advance!

suhrig commented 1 year ago

Arriba reports the names and IDs of the fused genes in its output file. You can look up their coordinates in the GTF fine. Is this the information you are looking for?

wiltbb commented 1 year ago

Thanke you,sir.I means,for example, if a gene on chromosome 1 fuses with a gene on chromosome 6, where is the newly created gene locate?

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Arriba reports the names and IDs of the fused genes in its output file. You can look up their coordinates in the GTF fine. Is this the information you are looking for?

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suhrig commented 1 year ago

It's not possible to name coordinates for a fusion gene. Fusion genes are a product of chromosomal rearrangements, which give rise to new chromosomes, which do not exist in the coordinate space of a normal chromosome set. For example, the famous BCR-ABL1 fusion is the product of a fusion between chromosomes 9 and 22. This so-called Philadelphia chromosome does not exist in the normal set of human chromosomes. Hence, you cannot say the fusion is located on chromosome xyz.

Sometimes, a fusion arises from a local rearrangement on one chromosome. This is true for most germline rearrangements and may be most relevant to your question, if you're interested in fusions that are common in the population. In this case, you can assume that the fusion is located roughly between the breakpoints. Please note, however, that Arriba was primarily designed for somatic fusion calling. Common germline variants are removed by Arriba's blacklist. Only rare germline variants are reported.