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Which AWS instance type for peak calling with ChIP-seq data?
We have generated ChIP-seq and RNA-seq datasets and are considering using Amazon's AWS cloud computing service to run various peak calling programs, assess...Last edited by mfeather; 09-20-2021, 07:30 PM. -
Can I use different cell lines of the same cell type from the same tissue?
Hi everyone,
I am an absolute novice to chip-seq and I have to plan a chip-seq experimnent involving the overexpression of a tanscription... -
chip-seq visualize tool IGV
Hello,
I tried to use IGV to visualize my chip-seq peak file.
Why it is so strange? The peak is not smooth?
Thanks... -
ChIP-seq library prep failed, NEBNext ULTRA DNA kit
Hi everyone,
I encountered an issue with histone modification ChIPseq library prep using the NEBNext Ultra DNA lib prep kit. Hope anyone...Last edited by DinaHer; 05-28-2019, 05:05 PM. -
Tag density count
Hi everyone,
I was wondering how to get the tag count number information from chip-seq data.
Thank you for your kind...Last edited by pico; 11-08-2018, 08:55 AM. -
Determining quality of ChIP-seq data
Hi all,
I am brand new to ChIP-seq, and I'm doing some practice data analysis. I'm trying to determine whether any trimming or post processing... -
Introducing Skymap: a single data matrix for each omic layer for each species
Skymap is a standalone database that aims to offer:
1. a single data matrix for each omic layer for each species that spans >200k sequencing... -
Problem with Bowtie 2
Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get... -
Problem with Bowtie 2
Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get... -
How to classify chIP-seq reads into gene bins?
Hello everyone!
I am very new to RNA-seq data analysis. Your help on how to accomplish the below task is highly appreciated! I will explain... -
common peaks and motifs between chip-seq replicates
Hi all!
I have 3 replicates of a chip-seq experiment, and after I used MACS for peak calling, I visualized the peaks on IGB. I see that there are... -
Quantifying mRNA levels
Hello,
How do we quantify the mRNA level of a gene present in a tissue? I am looking for the absolute mRNA levels of certain genes present... -
ChIP seq DNA starting material
Hello,
I'm new in the ChIP-seq field and had issues with my first experiment. I started with 5 ng of ChIP-DNA (as measured with Qubit, bioanalyser... -
Chipseq - Watson and Crick strand
Hi,
I am reading about CHIPseq from this paper and I encountered the following paragraph
Can anybody please explain how background...Last edited by New2Bioinfo; 12-08-2016, 05:54 AM. Reason: Earlier doubt resolved but new doubt in same topic. -
Training in Creating Plots, Graphs and Maps using R @ NIH, USA, Nov 15-17,2016
Training in Creating Plots, Graphs and Maps using R
Nov 15-17, 2016
Where?
National Institutes of Health...
