Hello!
I am struggling with non specific peaks called by macs2 around centromeric regions in my ChIP-seq data. A lot of reads map around...
14 results in 0.0022 seconds.
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ChIP-seq peaks in centromeric regions
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MACS2 output on Galaxy not readbale by BedTools on Galaxy
Hi!
I am getting the following error with Galaxy (need to get an answer specifically for Galaxy; without Galaxy I am not getting this error):... -
Macs2 Combining PE & SE
Hi Folks,
I am trying to use macs2 to call peaks then utilize idr2 to identify the final peak list. I have three biological replicates,... -
Negative pileup in MACS?
I am using MACS2 on ChIP-seq data. In the resulting <name>_peaks.xls file, I had understood the "pileup" column to be something like the... -
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 fails to create *_treat_pvalue.bdg
Hi all,
Thanks in advance for any help. I'm currently using MACS2 and trying to generate p-value tracks for some ChIP seq data as compared... -
MACS: ChIP and control with different tag size
Hi,
I am using MACS2 for ChIP-seq peak calling.
I have a treatment file with original reads of 51bp. Before alignment, the reads... -
Duplicate peaks in MACS2 narrowPeak output
Hi Everyone,
Has anyone noticed that MACS2 occasionally outputs duplicate peaks in the .narrowPeak output? There peaks have the exact same... -
How does MACS2 treat paired-end reads?
Hi all,
I cannot find good documentation on MACS2 and I do not understand how it treats paired-end data. I can see that I can use -f BAMPE to indicate... -
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... -
MACS2 bdgdiff output empty
Hi all,
I am trying to run macs2 bdgdiff
my command line
macs2 bdgdiff --t1 KO_treat_pileup.bdg --c1 KO_control_lambda.bdg... -
MACS2 installation problem
I am trying to install MACS2 on a computer running OSX 10.9.2. I have Python 2.7.5 and numpy is properly installed. I get the error message below. ... -
Double peaks for BOTH forward and reverse tags in macs2 model of Chip-seq data - shal
I analysed 3 chip-seq replicates (each with its own input control) using macs2. For two of the samples the model produced by macs2 looked fine. I am pasting... -
MACS2 ChIP-SEQ ANALYSIS WITH BIOLOGICAL REPLICATES
I am having problems with the broad mark H3K27me3, my biological replicates and identifying differential enrichment between treatment groups
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