User: shangyuan5000

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Posts by shangyuan5000

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Comment: C: Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using refer
... An update to my data: I tried kmers setting to 13,17 and 19, respectively. For 13, only 5.6% mapping rate; For k=17, ~49% mapping rate; for k=19, ~35% mapping rate. I also tried to exclude ncRNA in the mapping, by setting k=17, the mapping rate did not change much, still ~49%. Note that, for both ...
written 3 months ago by shangyuan500010
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Comment: C: Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using refer
... I have exactly the same question, short read length(=36) and very low mapping rates (~9.5%). I used cDNA to generate my index file and run salmon in quasi-mapping mode. For the low mapping rates, there were suggestions that I should include rRNA and build the index file from gtf file.(https://ww ...
written 3 months ago by shangyuan500010
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Comment: C: Signaling in PC3 and PC4
... Thanks, Kevin. My PC1 and PC2 does not separate the samples by groups, and I have no idea what they are separating since all samples were coming from the same batch as I was told. I will follow your example first and see what's coming out. To look into the loadings seems to be a really good idea. T ...
written 6 months ago by shangyuan500010
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Signaling in PC3 and PC4
... Hi, I have for group conditions and I run PCA analysis in DESeq2. After trying different PCs in the PCA plot, I found that PC3 and PC4 plot could well separate my samples: https://ibb.co/d5mpHn ![PCA analysis PC3 and PC4][1] [1]: https://ibb.co/d5mpHn I think that means my signaling probably ...
rna-seq written 6 months ago by shangyuan500010 • updated 6 months ago by Kevin Blighe28k

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