User: dustar1986

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dustar1986330
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Posts by dustar1986

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Comment: C: DESeq2 Design with Three Interactions
... For the last 4 contrasts, I'm trying to look at interaction effects between two factors instead of the main effect of each factor. Punch me if I'm wrong... ...
written 4.9 years ago by dustar1986330
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Comment: C: DESeq2 Design with Three Interactions
... Thanks russhh. From the code above if I've done them correctly, there is a small interaction of phenotype and treatment in both male and female (influence about 10 genes), including the key gene lead to tumour. There is also a small interaction of sex and phenotype (affected 50 genes). No interacti ...
written 4.9 years ago by dustar1986330
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DESeq2 Design with Three Interactions
... Hi DESeq2 Community, I'm currently working on a comparison of drug effects on tumour and wild-type cells. I have tumour cells from 4 patients (2 males and 2 females) and normal cells from 4 normal people (2 males and 2 females). Each cell sample was treated under three different conditions: plain c ...
R rna-seq written 4.9 years ago by dustar1986330
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Answer: A: What's the best way to map CAGE-seq data to the genome?
... Worked out. Fantom5 uses its own aligner Delve: http://fantom.gsc.riken.jp/5/suppl/delve/delve.tgz ...
written 6.8 years ago by dustar1986330 • updated 13 months ago by Ram32k
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Comment: C: What's the best way to map CAGE-seq data to the genome?
... Thanks for your detailed explanation, Floris. That is extremely helpful for me. I think I really should download the bam file (mm9) and re-map them to mm10. ...
written 6.8 years ago by dustar1986330
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What's the best way to map CAGE-seq data to the genome?
... Hi, I've just downloaded several mouse CAGE-seq data from FANTOM5 database.  I tried using bowtie2 default setting to map those rdna.fa files to mm10. And I found a quite low mapping rate around 40% with the majority reads hit more than 1 locus.   I'm totally new to CAGE-seq data. Please forgive ...
cage-seq bowtie written 6.8 years ago by dustar1986330 • updated 6.0 years ago by Vandelnokk10
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Comment: C: Which statistics should be applied to determine whether a region is differential
... Thanks indeed! ...
written 6.9 years ago by dustar1986330
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Comment: C: Which statistics should be applied to determine whether a region is differential
... Thanks for your quick and detailed reply, Devon. This is really irradiative to me. I've read the mannual of BiSeq and methylKit. MethylKit seems focusing more on the comparison between simple sites. BiSeq could give what I need. However, what I have is the whole genome BS-seq data instead of RRBS. ...
written 6.9 years ago by dustar1986330 • updated 14 months ago by Ram32k
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Which statistics should be applied to determine whether a region is differentially methylated or not?
... Hi,   I've got bisulfite-sequencing data for two differentiation stages. The raw data was mapped using Bismark. For each CpG site, the methylation ratio was marked as "A/B" (A methylated reads vs B unmethylated reads for this site).   Now I want to compare the overall methyaltion of a certain re ...
bs-seq bismark statistics written 6.9 years ago by dustar1986330
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Comment: C: Which Statistics Should Be Applied To Determine Whether A Certain Motif Is Signi
... Got it. Thanks a lot. ...
written 6.9 years ago by dustar1986330

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