User: lkw222

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lkw22230
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Posts by lkw222

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Comment: C: Setting Up Model in DeSeq2
... Well, my concern is this. There's appears to be some large variation between samples that is not accounted for by the diet (here U vs. AO) or the time point (0, 60, 240). Also the histogram of the p values is not what I expect to see? I've added links to graphs to the original question. ...
written 9 days ago by lkw22230
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Comment: C: Setting Up Model in DeSeq2
... Thanks for pointing me there - I was able to use the grouping variable tactic. Then I can compare group C_time0 vs group A_time0 and so on and so forth. The only problem is, when I pull out the results using results(dds, contrast = c("group", "C_time0", "A_time0") all the adjusted p values are eith ...
written 9 days ago by lkw22230
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Setting Up Model in DeSeq2
... I usually stick to genome seq data, so this is my first time using deseq2. I have RNAseq data from Drosophila that were fed either a control diet (C) or supplemented diet (A) while under going physiological stress. They were sequenced at three time points during the experiment. I have the following ...
deseq2 rna-seq differential expression htseqcount written 10 days ago by lkw22230 • updated 9 days ago by genomax70k
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Help with species level ID (L 7) in qiime
... Looking for some recommendations. A former coworker left me with a table resulting from, I believe, the summarize taxa workflow in qiime. The table I have has the following columns - sample ID, time ID, treatment ID, number with no blast hits, k__Archaea;p__Crenarchaeota, k__Archaea;p__Euryarchaeo ...
microbiome metagenomics otu written 8 months ago by lkw22230
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Evaluation of PacBio only de novo assembly
... Does anyone have experience using validation/evaluation methods (other than basic statistics like N50) for a PacBio only de novo assembly? What would you recommend? Note: I don't have multiple assemblies to compare, just want to try to do some validation of a single de novo assembly. ...
de novo assembly assembly genome pacbio sequencing written 2.8 years ago by lkw22230 • updated 2.8 years ago by Rohit1.4k
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Answer: A: Cummerbund Returns 0 Sample
... Did either of you find a solution to this problem? I am having the same issue as in the original post. ...
written 3.2 years ago by lkw22230
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Answer: A: error while buliding database in readCufflinks in CummeRbund package
... I am having the some problem. Did you find a solution? ...
written 3.2 years ago by lkw22230
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Genotype dosage from VCF genotype likelihoods
... Is it possible to create a file of genotype dosages from a VCF using the phred-scale likelihoods (PL) given for each possible genotype? For example the genotype call: 1 497 . C T 1882.89 PASS GT:AD:DP:GQ:PL 0/0:3,0:3:0:0,0,45 where the PL for 0/0 is 0 and fo ...
vcf genotype dosage rna-seq written 3.4 years ago by lkw22230 • updated 3.0 years ago by Biostar ♦♦ 20
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Speeding up NUCmer for de novo contig to reference alignment
... I have a de novo assembled mammalian genome (~300,000 contigs) that I want to align to a closely related existing reference genome using NUCmer from the MUMmer package. Subsequently, given the Coords output of the NUCmer alignment, I want to use something like OSLay to order and stitch together the ...
assembly alignment sequencing written 3.5 years ago by lkw22230 • updated 3.5 years ago by ALchEmiXt1.9k
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Comment: C: samtools mpileup memory leakage
... Thanks for the answer and reference. And yes, there are a lot of region of in my BED file because my reference genome is in about 300,000 pieces! Time to update to 1.3. ...
written 3.5 years ago by lkw22230

Latest awards to lkw222

Popular Question 8 months ago, created a question with more than 1,000 views. For Genotype dosage from VCF genotype likelihoods
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Genotype dosage from VCF genotype likelihoods
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Speeding up NUCmer for de novo contig to reference alignment
Popular Question 2.2 years ago, created a question with more than 1,000 views. For samtools mpileup memory leakage

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