User: leaodel

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leaodel60
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Posts by leaodel

<prev • 9 results • page 1 of 1 • next >
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Answer: A: WGCNA soft thresholding problem
... Hi catagui, I was having the same issue and setting `dataIsExpr = T` on `pickSoftThreshold()` solved things for me. Hope it helps! ...
written 9 days ago by leaodel60
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Answer: A: I meet some problem for using Deseq2.
... Hi, codezy. You should really dive into DESeq2's tutorial, it's an essential resource for learning. With that being said, when you have files from HTSeq you should use another function to import your samples. Try this: Create a variable with the file's path: dir <- "~/pathtoyourfiles/" Add ...
written 5 weeks ago by leaodel60
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Answer: A: 16S rRNA classification pipeline
... Hi Sus, I would try the [BMP pipeline][1], they provide a detailed pipeline that you can use as it is or construct yours from theirs. You can find a detailed guide for rRNA 16/18 and ITS data analysis. Good luck! [1]: https://www.brmicrobiome.org/target ...
written 5 weeks ago by leaodel60
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Comment: C: Somatic vs Germline Variant Calling
... I agree with you. I was referring to germline variant call, should've made that clear. My understanding is that you'd need child-parent comparison if you want to find new variants or in a clinical setup. I just have some RNA-seq samples and I want to compare their SNPs. Bottom line, the basic assum ...
written 4 months ago by leaodel60
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Comment: C: Somatic vs Germline Variant Calling
... Thanks, RamRS. I do understand that 'software is dumb' but there must be some underlying assumption to call either somatic or germline variants other than experiment design. Otherwise, we wouldn't need distinct software (I.e., HaplotypeCaller for germline and Mutect2 for somatic, both from GATK). P ...
written 4 months ago by leaodel60
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Comment: C: Somatic vs Germline Variant Calling
... Aside from the conceptual answers on what is somatic and germline, I would very much like to know how a software can tell apart germline and somatic. I know that tools are specific for either somatic or germline variant calling, but other than that what are the basic assumptions that these tools rel ...
written 4 months ago by leaodel60
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Comment: A: download repeats annotation file
... If you have a reference genome, I would give a try to [RepeatMasker][1]. One of the outputs is a bed3-like file that you can easily subset to get an annotation file. They also have a web-server where you could try a toy example. [1]: http://www.repeatmasker.org ...
written 4 months ago by leaodel60
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Comment: C: Heatmap.2 R for differentially expressed genes DeSEQ2
... On the previous line you're missing a comma to index rld by topVarGenes in two dimension way: # use the log transform on the data set matrix <- assay(rld)[ topVarGenes, ] matrix <- matrix - rowMeans(matrix) ...
written 10 months ago by leaodel60
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Best-suited unit of expression to perform between-sample comparison
... Dear biostars community, I'm having some doubts regarding which measure is ideal for reporting expression values and I thought you could help me with your experience. I've been dealing with RNA-seq data from two projects now (one single end and other project paired-end reads) and I want to choose ...
normalization expression value rna-seq written 10 months ago by leaodel60 • updated 10 months ago by Carlo Yague4.4k

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Student 28 days ago, asked a question with at least 3 up-votes. For Best-suited unit of expression to perform between-sample comparison

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