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Hi there,
Thank you again for creating this wonderful tool! I had a question regarding your fusion gene analysis in your recent biorxiv paper: https://www.biorxiv.org/content/10.1101/2021.04.21.440…
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I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptide…
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Thank you for the great tool.
I am wondering if there is anyway to generate a Fasta based on the gene fusion output. I would like to quantify TPMs with Salmon/Kallisto which require a Fasta version…
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Dear dr, Uhrig,
I have short read samples, one of them we know the CIC-DUX4 fusion is present. Alignment was done with STAR. After running Arriba on the generated BAM file, the expected fusion was …
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Wicked fast indeed! Are there any plans to extend salmon to also detect gene fusion events? There isn't a fast and accurate way to do that yet, only approaches requiring full alignments. Most often a …
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Hi there,
I apologize for the naive question I'm about to ask, but I've been struggling with this for a week and would appreciate some help. I created a custom gene index using a FASTA file of fusi…
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Hello, are there any plans to also include gene fusion detection in Hisat2, or will that be left to other tools working on the output Samfiles?
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Thank you for creating a nice software!
I'm wondering if it makes sense to exclude genes with poor prediction accuracy from prediction model as it could be noisy information.
Do you have any idea?
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Add 7316-1106 and 7316-3000 back to hope subcohort, except for proteomics. Use the attached file from Pei.
[master_11032023 (1).txt](https://github.com/user-attachments/files/15892642/master_11032023…
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Hi, Sigven, Now PCGR can analysis SNV/INDEl and CNA. would you like to add gene fusion function in the future?
Another question is that given tumor/normal raw data(fastq), can you recommend some pi…
pl618 updated
9 months ago