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Arriba and STARfuison align #239
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Hi, could you kindly pick one read which is aligned by STAR-Fusion but not by Arriba and extract the paired-end reads from the Arriba BAM file using for example |
Thanks for your reply. I grep one read here.
STARfusion
|
Thanks for providing the details. Without any further evidence, I would argue that Arriba is right here. It finds a better alignment than STAR-Fusion. The alignment proposed by Arriba is linear and even matches an annotated transcript of a gene perfectly (namely, The reason why STAR-Fusion prefers the chimeric alignment over the linear one is simply because it uses a very low value for Do you have any reason to believe that this fusion is real? For example, do you have structural variants from whole-genome sequencing data to confirm this fusion? If not, then I find it likely that the fusion prediction made by STAR-Fusion is wrong in this case. |
Thank you, and I will provide further information if I have any. |
In the end, I could not further validate this sample. However, the same fusion event was detected in the WBC of the patient, leading me to believe that STARfusion's fusion event is erroneous. Thank you for your assistance. |
Thanks for your feedback! |
Hi,
The picture below illustrates the differences between the alignment results of Arriba (v2.4.0, STAR2.7.8a) and Starfusion (v1.10.0, STAR2.7.8a). In Starfusion's BAM file, there are numerous softclip reads that support the TIMM23--LINC00843 fusion events (chr10:51606988--chr10:51732772). It appears that the parameter settings used by Arriba's STAR alignment discarded many of these reads.
Could you provide me with some suggestions?
arriba code(use the raw run_arriba.sh script)
STARfusion code
Best,
xiucz
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