17 results in 0.0050 seconds.
-
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. -
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... -
Can or should we perform feature counting with `bedtools intersect -c`?
I have the following BAM file and a annotation file.
What I want to do is to calculate reads count in
I can do it with the following three... -
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. -
Too few peaks in MACS2
Hi everyone, I'm trying to call peaks with macs2 but run into the next warning when doing so:
"WARNING @ Tue, 14 Jun 2016 20:52:53:... -
MACS2 broad peak calling
Is there an explanation for what the broad-cutoff means for broad peak calling for MACS. In the documentation for MACS they say it is a q-value cutoff... -
Next gen sequencing analysis - for small genomes
Hi,
I am working on an organism with a small genome (Toxoplasma gondii, 65 Mbp). With ChIP-seq, we naturally tend to get very high sequence... -
Peak calling tools ChIP-seq
Dear all,
What are the most widely used peak calling tools for ChIP-seq data at the moment?
Thanks,
Eunice -
Calling narrow and broad peaks from ChIP-Seq data - Benchmarking study
Know about the state-of-the-art algorithms implemented in Strand NGS for detecting the binding sites of transcription factor (narrow peaks) and enriched... -
peak identification with macs2 for small RNA data
Hello,
I have illumina data from small RNAs and am using MACS2 to identify peaks in read mapping. (Read mapping done with bowtie1.) This... -
MACS2 callpeak AttributeError: 'Namespace'
Hey all,
I am trying to run macs2 callpeak, with this command line
GEN_SIZE=0.4379e9
PVALUE=1e-5
macs2 callpeak -t... -
diffReps - ChIP-seq differential analysis package
Dear colleagues,
I'd like to introduce you to diffReps -- a ChIP-seq differential analysis package that my group developed.
... -
RNAseq peak calling
I have some sncRNA seq datasets and would like to identify differentially expressed regions.
The problem is that the interesting regions... -
Peak confidence in FindPeaks
Hello I am using Find Peaks without control data, is there any option so I can get statistical confidence on my peaks?. I see that the Min. cov. allowed... -
Few Peaks
I am analyzing a ChIP-Seq data set for another lab. The sequencing seems to have gone quite well, with a high depth of coverage (more than 4million mapped...
