User: leaodel

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leaodel10
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EUA
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1 month ago
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4 years, 1 month ago
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Posts by leaodel

<prev • 6 results • page 1 of 1 • next >
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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 8 weeks ago by leaodel10
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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 8 weeks ago by leaodel10
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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 8 weeks ago by leaodel10
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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 11 weeks ago by leaodel10
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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 8 months ago by leaodel10
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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 8 months ago by leaodel10 • updated 8 months ago by Carlo Yague4.3k

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