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Calling DMR (DMLtest with smoothing) from a 2 vs. 2 WGBS data costs about 20 hrs, no matter the workers= 200 or workers=100 in MulticoreParam. (The total cores in the machine are 256.)
The real CPU u…
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It's mentioned in the [special columns section](http://looper.readthedocs.io/en/latest/define-your-project.html?#special-columns) of the project definition docs that `sample_name` should be a unique i…
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Hi,
Thanks for the methylation analysis pipeline.
I was testing a human WGBS data with msPIPE, and I used UCSC hg38 for reference. When running with run_MethylSeekR.pl, I got the following error…
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Hello;
I have tested the BSseeker2 for my data, and run the Bismark and BSMAP for the same data.
The parameters of BSMAP and Bismark was default. The align step of BSseeker is default, an…
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This part of the pipeline always fails, for all samples. After a few different runs with different data sets, this always happens. However, the stats files actually _are_ generated, but I'm not sure w…
kubu4 updated
2 years ago
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Hello,
I was wondering whether BatMeth2 can also directly output the alignments in BAM format? Currently I have to sort the alignments with samtools, but the SAM file is really large and creates prob…
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Dear all,
I am plotting WGBS data over predefined regions. This is command I used:
```
computeMatrix reference-point -R regions.bed \
-S DNA_3.bw \
DNA_4.b…
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Hello,
Thank you for developing EpiSCORE. I have been using it to calculate the proportion of cell types making up healthy prostate as well as prostate tumour samples and so have been using mrefPro…
ghost updated
2 years ago
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Dear all,
I am plotting WGBS data over predefined regions. This is command I used:
```
computeMatrix reference-point -R regions.bed \
-S DNA_3.bw \
DNA_4.bw…
mvukk updated
2 years ago
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I installed using pip3. I am trying to run the CpG_aggregation.py test. I downloaded the test files, and am now running `CpG_aggregation.py -b hg19.RefSeq.union.1Kpromoter.bed.gz -i test_03_RRBS.bed …