User: shunyip

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shunyip180
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Posts by shunyip

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Comment: C: filtering or not the gtf annotation file from ncRNA, tRNA, and rRNA before mappi
... I believe you need to check whether those 5500 extra DE are all nc, t or r RNAs. ...
written 2.2 years ago by shunyip180
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Answer: A: human geneome alignment RNAseq
... [This][1] teaches you how to create a gene annotation file with rRNA in it. In short, in [UCSC table browser][2], choose "All Tables" under "group" and choose "rmsk" under "table". [1]: http://onetipperday.sterding.com/2012/08/how-to-get-trnarrnamitochondrial-gene.html [2]: https://genome.uc ...
written 2.2 years ago by shunyip180
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Comment: C: Help with Trimmomatic 0.36 Error
... [seqtk][1] may be able to help you. It can convert multi-line FASTQ to 4-line FASTQ. [1]: https://github.com/lh3/seqtk ...
written 2.2 years ago by shunyip180
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Comment: C: Normalization read counts scRNA seq with spike ins
... Your question sounds similar to [SAMstrt][1]. Maybe you can take a look. [1]: https://www.ncbi.nlm.nih.gov/pubmed/23995393 ...
written 2.2 years ago by shunyip180
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Comment: C: Problems installing ete3 using conda
... I had a similar error from installing a different package. I solved it by removing everything that are in conflict (including python itself), and then installing what I need (in your case, ete3). This way, conda should also install python again because it's one of the dependencies. I hope this help ...
written 2.2 years ago by shunyip180
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Comment: C: How to compare two groups of 3 samples
... It shouldn't matter. Um.. did you filter all signals where one of the samples is zero or has very low read count? From personal experience, when I see bimodal in this situation, one of the peaks could be caused by low count genes. Usually, after I filter it, it will become normal. ...
written 2.2 years ago by shunyip180
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Comment: C: How to compare two groups of 3 samples
... You might need to normalize your expression data then. Are you using CPM or TPM? ...
written 2.2 years ago by shunyip180
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Comment: C: Analysis of methylation values
... Maybe you could use Spearman correlation coefficient. ...
written 2.2 years ago by shunyip180
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Comment: C: How to compare two groups of 3 samples
... If you do not have replicates, you will have to assume that the sample's expression values are all accurate. Instead of performing a t test gene by gene, I would suggest calculating the fold change of all genes. Then, identify genes with significantly high log2 fold changes as DEG. This way, you c ...
written 2.2 years ago by shunyip180
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Answer: A: How to compare two groups of 3 samples
... You can look at the manuals of several Bioconductor tools, such as [limma][1], [edgeR][2] and [DESeq2][3]. [1]: https://bioconductor.org/packages/release/bioc/html/limma.html [2]: https://bioconductor.org/packages/release/bioc/html/edgeR.html [3]: https://bioconductor.org/packages/release/bi ...
written 2.2 years ago by shunyip180

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