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MeDIP seq data analysis (identify DMR)

macs chip-seq methylation medip methylqa written 3 months ago by iridha • 0

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103

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MeDIP seq data analysis

peak peak calling aligment medip methylation written 4 months ago by iridha • 0 • updated 4 months ago by genomax ♦ 85k

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171

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How comparable is MeDIP-Seq with RRBS/WGBS?

wgbs medip rrbs written 8 months ago by Deepak Tanwar • 4.0k

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794

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QSEA package - Enrichement parameters choice (addEnrichmentParameters)

medips qsea methylation medip written 2.7 years ago by lech.kaczmarczyk • 50

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991

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Peak calling on MeDIP data

medip written 2.7 years ago by lech.kaczmarczyk • 50

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683

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Low reads mapping in methylation sequencing

medip mapping written 3.0 years ago by SJ Basu • 30 • updated 3.0 years ago by Chris Miller ♦ 21k

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849

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Comparison of MeDIP data with transcriptomics expression data

medip rna seq written 3.3 years ago by saripalligautam86 • 0

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1.5k

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Comparison of two MeDip data sets

chip-seq medip hmedip written 4.4 years ago by florian.noack • 20

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1.8k

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Convert MEDIP-seq RMS values into AMS using MEDIP

methylation medip written 5.3 years ago by rdbcasillas11 • 0 • updated 5.3 years ago by Devon Ryan ♦ 95k

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Recent Replies

C: Protocol for genome assembly of Sars-cov-2 sequences by genomax ♦ 85k
You should be able to use `SPAdes` or even `tadpole.sh` from BBMap suite for the assembly. Method...
A: Vg call in a specific region by glenn.hickey • 140
It's less necessary to break the graph into tiny chunks with `vg chunk -p`. Here's an example on...
C: Error while running CPAT by grant.hovhannisyan • 2.0k
it seems you did´t use conda. first install miniconda (it is a package manager) https://docs.con...
C: Convert Logp value to P value by RamRS ♦ 27k
Your base is probably not 2 then. The `**` and `^` operators are equivalent - now that Antonio's ...
A: Why Salmon produces very different quantification results compared with featureC by jordi.planells • 160
As far as I know, salmon takes multimappers into account, maybe there you find the difference. Co...
C: Russian universities for the study of biomedicine by grigoryangeorg • 30
thank you very much, it helped me a lot
C: Robinson-Foulds Distance : Number Of Trees At Distance K From A Fixed Tree by leonardini • 0
The paper is now published and available here: https://www.sciencedirect.com/science/article/pii/...
A: RStudio Pheatmap: sort DEG by logFC by caggtaagtat • 1.1k
Hi, I also think, you use DESeq2. So if thats true, you could do something like this: For the L...
C: RStudio Pheatmap: sort DEG by logFC by cpad0112 ♦ 13k
From the code, it seems earlier dev used DESeq2 analysis. Please follow the manual of DEseq2 here...
C: bowtie2 '-a' does not return all alignments by genomax ♦ 85k
Try `bbmap.sh` as an alternate. It has a `ambig=all` option that should report all possible align...
C: RStudio Pheatmap: sort DEG by logFC by antonioggsousa • 460
Hi, Can you post the code that you've used before and print the first few lines of your data? ...
A: Why Salmon produces very different quantification results compared with featureC by caggtaagtat • 1.1k
Apparantly, it is not uncommon for lncRNA transcripts to overlap with coding genes. Maybe the dif...

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