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Comment: From TPM to raw counts
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Gama313
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Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link:
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Comment: From TPM to raw counts
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Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
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My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
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Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
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In principle, the TPM formula can be reverted, see the timeless post
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You're right, I wasn't explaining the problem clearly. Thanks for the directions!
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All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
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Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
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Sorry for the delay in expressing my thanks.
I found the advice to look at the information from MySQL very useful.
I will also refer to t…
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I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
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In most cases error-correction should take care of error-spawned fake minor alleles, though...
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It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
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I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
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AMARU
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Can you post the commands you used?
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Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation
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version 2.3.6