More posts like this
-
Tools for eQTL and somatic mutation analysis of RNA-seq data
written by malonzm1 •Hi, Does anybody have experience performing eQTL analysis and/or somatic mutation analysis of bulk RNA-seq data (without normal sample)? What tool/s/pipeline did you use? Thanks …
-
macs2 bdgpeakcall only gives a few peaks
written by baijiangshan9726 •Hi, all. I want to call peaks from bigwig file. I first transfer bigwig to bedgraph by using "bigWigToBedGraph A.bw A.bedgraph", then I use "macs2 …
-
circular RNA analysis workflow
written by aminijavad4 •Hi, I need to analyse circular RNA in RNA-seq data and get circular RNA differentiation expression. I am familiar with bulk RNA-seq data analysis but …
-
Annotate peaks and G quadruplex
written by ab2063 •I am a beginner in R. I have ChIP peaks and G quadruplex hg19 data. I want to annotate these peaks with G quadruplex, in …
-
plot tss profile
written by ab2063 •I would like to plot the typical TSS profile using the ratios for Watson and Crick strand around my TSS (something like the figure1e of …
-
RIP-Seq data analysis
written by flyguymail22 •Hi I have performed a RIP-Seq experiment, that is RNA Immunoprecipitation followed by RNA sequencing. Does anyone know of an established pipeline or tool as …
-
repli-seq analysis pipeline
written by 2nellyHi all, https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/repli-seq.html Does anybody know a good pipeline to analyze repli-seq data (please see the link above) in order to find origins peaks? I …
-
Problems with MACS ChIP-Seq peak calling
written by dcheng1 •I downloaded raw data in GEO and analyzed it following general ChIP-Seq pipeline: trimming adapter, mapping and calling peaks. However, when compared with bigwig files …
-
Pipeline for detecting (TF) Chip-seq peaks in transposable elements?
written by BiojlHi, Anyone knows a good pipeline to call TFBS peaks using chip-seq data in transposable elements? Most of the traditional pipelines rely on uniquely mapped …
-
sicer chip seq analysis
written by robertacar •Hi everyone, I'm new in ChiP-seq analysis. I'm using SICER to analyze histone modification data with a control library. I have some doubts regarding the …
Past thread of interest: repli-seq analysis pipeline
I did see that. But wasn't of much help. Do you know of some other detailed pipeline/tutorial or have some suggestions.