User: raywong.chn

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raywong.chn10
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Posts by raywong.chn

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Answer: A: Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... Problem solved. It turns out that this is due to building the salmon index with ensembl genome fasta, which contains plenty of gene duplicates on haplotype chromosomes. Switching to GENCODE should resolve the issue, as suggested in this thread: [https://support.bioconductor.org/p/p134094/#p134255 ...
written 4 days ago by raywong.chn10
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Comment: C: Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... @swbarnes2 Yes you're right. I guess what I'm really concerned about is how to interpret this at the biological level. If we believe these gene polymorphism to be *bona fide* mapping, how did it happen in a cultured cell line? ...
written 11 days ago by raywong.chn10
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Comment: C: Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... @ponganta thanks for the input and @ATpoint thanks a lot for clarifying things up. There are 490 genes containing calls to multiple genomic loci. The number of ambiguous calls for each gene varies, ranging from 2-7. ...
written 12 days ago by raywong.chn10
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Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... We're analyzing RNAseq data with a pipeline consisting of Salmon, tximeta, and DESeq2. We have a multi-factorial experimental design, and the experiment was performed on cell lines. On thing that surprised us is that in the result output, we observe many gene polymorphisms. For example, for gene ...
alignment rna-seq written 12 days ago by raywong.chn10

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