MACS
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macs3-project
MACS -- Model-based Analysis of ChIP-Seq
Hello, MACS2 stalls at the following line: ``` #3 Pre-compute pvalue-qvalue table... ``` I have two BAM files, one converted to BAM from Bowtie2 output and the other which has...
Hi, I would like to detect differential peaks between two different conditions by `macs2 bdgdiff` and use `-d1` depth_condition1 `-d2` depth_condition2. But I don't know whether to normalize the data...
Hello, I have run MACS3 to call peaks from IP and input files, and obtained the peaks and related fold enrichment. **Peaks** are filtered based on fold enrichment>5 and q...
Hi I am comparing different peak calling parameters for pair-end ATACseq data. I noticed that for the same peak called with different parameters has different q Values. Here are the...
Hi, I'm having trouble finding any explanation of the bdgdiff log likelihood ratios and I am wondering: (I followed the instructions in the Wiki for identifying differential sites) - are...
Hi. I received the following error when performing `macs2 callpeaks` ``` INFO @ Wed, 24 Oct 2018 17:15:52: #1.2 read input tags... INFO @ Wed, 24 Oct 2018 17:15:52: #1...
Hi, This is a general question about the `-slocal` and `-llocal` parameters. I wonder under what condition would the callpeak function uses `-slocal` and when `-llocal` is used? Since I'm...
**Use case** A clear and concise description of what the use case is. For example: my data is from [...] **Describe the problem** A clear and concise description of what...
**Use case** I have a series of ChIP-seq samples that I eventually want to perform differential peak calling and motif enrichment analysis upon between different treatment groups (and input). **Describe...
Hi, I had a query about calculating the genome size needed for the MACS --gsize option. **Use case** I shall be using genomes not listed in your documentation and so...
