26 results in 0.0041 seconds.
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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... -
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... -
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... -
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... -
MACS "Exception: Can't detect format!" error
I'm running MACS on some .bam files, and I'm coming across this error on one particular .bam file (but not all .bam files) and I'm not sure what to do... -
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... -
ChIP-Seq Analysis and Visualization using Galaxy and IGB. (January 28, 11:30am-12pm E
“Focus on a Feature: ChIP-Seq Analysis and Visualization using Galaxy and IGB.”
This Focus on a Feature has finished. The recording...Last edited by Nowlan Freese; 02-08-2015, 01:14 PM. -
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. ... -
Chip-seq tags of unequal length - is this a problem for macs?
I have a chip-seq sample where a significant proportion of the reads have low quality bases at the end. Trimming these bases using sickle or Trimmomatic... -
Large number of MACS negative peaks
I have a TF chip-seq study with two types of replicates:- 2 Flag+TF samples, each with a corresponding IP control (Type A)
- 2 Flag- samples, each with
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ImportError of MACS 1.4: cannot import name opt_validate
ImportError of MACS 1.4: cannot import name opt_validate
I installed the MACS-1.4.2 by using command:
python setup.py...Last edited by bigdataage; 12-10-2013, 03:23 AM. -
Weird MACS behavior
I am trying to run macs14 with sam files from paired-end data + control. Macs14 returns "No such file":
...Code:sb7904313:line2 $ macs14 -t /Volumes/Data/G6L2_G6L3/s5/clean_paired_sample.sam -c /Volumes/Data/G6L2_G6L3/s11/clean_paired_sample.sam
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Combination of paired-end and single-end samples in Chip-seq TF study
I have 2 batches of chip-seq samples:
(A) One biological SE replicate
This batch, actually, consists of 4 SE Chip-seq samples...Last edited by feralBiologist; 11-23-2013, 11:51 AM. -
For ChIP-seq, maximal coverage at a peak?
For ChIP-seq data, what is the maximal coverage at a peak? How to calculate it? Thank you!!!
The coverage is defined as :
Number of...Last edited by xxatbio; 08-12-2013, 01:05 AM. -
MBDseq with or without input DNA control
I'm validating a MBD-seq library and having difficulty understanding the need for a non-enriched input sample. We're using a MACS based approach to analyse...
