MACS
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macs3-project
MACS -- Model-based Analysis of ChIP-Seq
Hi folks, We had trouble processing some data with 2.1.1.20160309 so we ran instead with 2.1.2.1. In another test we are seeing what look like significant differences in results between...
Hi, I'm running macs2 through miniconda3 on a shared server. It looks like macs2 by default uses the maximum number of available cores to spawn subprocesses during peak calling, thereby...
**Use case** I would love to install MACS3 directly via the conda manager to keep things as clean as possible. **Describe the problem** The link to the bioconda page has...
When running on a broadpeak file, callvar does the following: ``` macs3 callvar -b Met.mRp.clN_peaks.broadPeak -t ~/results/chromap/merged_replicate/met_filtered.bam --outdir results/var -o variants.vcf ``` File "MACS3/Signal/RACollection.pyx", line 358, in MACS3.Signal.RACollection.RACollection.get_PosReadsInfo_ref_pos File "MACS3/Signal/RACollection.pyx",...
**Use case** My data consist of BAM paired-end files already filtered by duplicates, mit reads, etc. (99% alingment) **Describe the problem** I tried to use this command in bash macs3...
I ran HMMRATAC on two samples that should be biological replicates. The quality difference between them is high, although the quality is far from ideal for both. However, the low...
**Describe the bug** callpeak function fails due to old glibc version during compilation of cython code (assumption) **To Reproduce** ``` pip install macs3=3.0.1 macs3 callpeak -t $BAMFILE -n 8h_3utr --nomodel...
I noticed that HMMRATAC does not seem to be deterministic. If I run it multiple times, sometimes I get a different number of peaks. I see that there is a...
Dear @taoliu Thank you for macs and for the constant improvements you have been adding. **Use case** I have some histone chip data on cancer cell lines where they were...
I have been using bigWig file from bdgcmp containing logFE values (compared ChIP signals against Input). As part of next step, I would like to use bdgpeakcall, where I am...
