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The Nature paper says that by using the software graph_peak_caller, we can do ChiP-Seq analysis on genome graphs. However, the original graph_peaker_caller paper says "Graph Peak Caller was developed …
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Hi,
Maybe I'm getting this totally wrong, but from the README file it seems that to annotate regulatory regions for each gene or region, you can either use a motif annotation generated by cluster-b…
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Hello,
I noticed that `Centromics` accept only one ChIP data alignment in bam format.
If this refered to the CenH data, how to use the control (input) data, or `Centromics` do not need control?
Tha…
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## **Description of bug**
I've installed caper and the pipeline in a conda environment and I'm trying to run it with example config/data from the repo thusly:
```
$ git clone https://github.com/e…
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Current implementation of ChIP-seq pipeline launches `sicer.sh` and filters its output through the pattern `['*sicer.log', '*.bed', '*rip.csv']`. However, `sicer.sh` used to have its own file filterin…
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I am testing one stereo-seq chip about 10K spots (bin50). The running time is too long:
model.train(device="cuda:0", sampler = "R")
```
0%| …
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Hi,
Has anyone tried CIDR to cluster ChIP-seq data?
Any recommendations on where to start with?
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Hi Sebastian,
Thanks for this useful tool!
1) I would like to plot computeMatrix file with the parameter --unscaled5prime or --unscaled3prime. Is it possible to include this in the Rseb?
2) Alt…
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With file names:
```
SRR1917137_GSM1635411_Ikaros_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
SRR1917139_GSM1635413_Brg1_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
SRR191714…