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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
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by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
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ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
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GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
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txema.heredia
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Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
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kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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Pierre Lindenbaum
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there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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egascon
• 0
It's a microarryay experiment, not RNASeq
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Pierre Lindenbaum
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https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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DGTool
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I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
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