User: dustar1986
dustar1986 • 330
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Posts by dustar1986
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... 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
dustar1986 • 330
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... 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
dustar1986 • 330
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... 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 ...
written 4.9 years ago by
dustar1986 • 330
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... Worked out. Fantom5 uses its own aligner Delve: http://fantom.gsc.riken.jp/5/suppl/delve/delve.tgz ...
written 6.8 years ago by
dustar1986 • 330
• updated
13 months ago by
Ram ♦ 32k
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... 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
dustar1986 • 330
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... 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 ...
written 6.8 years ago by
dustar1986 • 330
• updated
6.0 years ago by
Vandelnokk • 10
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... Thanks indeed!
...
written 6.9 years ago by
dustar1986 • 330
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... 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
dustar1986 • 330
• updated
14 months ago by
Ram ♦ 32k
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... 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 ...
written 6.9 years ago by
dustar1986 • 330
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... Got it. Thanks a lot.
...
written 6.9 years ago by
dustar1986 • 330
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