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I think the trimmomatic call needs this: -Xmx512M , e.g. `java -Xmx512M -jar ...`
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Hi Felix,
Sorry if this is the wrong forum to post this question...I don't think it is an issue as more likely I just don't understand this.
Can you please explain how the bam alignments relate …
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Hi,
can defiant analysis Difference Methylation on ROI？For example, I want to analysis difference methylation of a set of immune response genes between two groups, the difference methylation …
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Hi Keegan, the paper introduced a very interesting idea and I'm curious to try it out.
Just one simple suggestion regarding the prerequisite packages: since I'm new to WGBS methylation data, I don…
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When running with **single-end reads**:
```bash
gemBS bsMap-report -j "pgp2/gembs.json" -i "pgp2/gembs_mapping1" -n "pgp2" -o "out"
```
I get the following error:
```bash
------------ Input…
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Is it just suit for WGBS of single cell ?
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It seems that when running tabulate like so:
`/home/john/toolshed-0.4.0/bwa-meth-0.10/bwameth.py tabulate --map-q 60 --bissnp /ex/BisSNP-0.82.2.jar --prefix Mm01.WGBS -t 10 --reference /ref/mm10.fa -…
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I have a follow-up question. It seems that the getMatrices.sh won't stop immediately even though the final matrices.mat file already exists, but I though it won't rewrite the existing file. How can I …
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Hi, I failed to run getMatrices.sh and got the error message: "Error using symengine
Unable to convert expression into double array." I didn't see symengine installed in the informMEdeps folder. Coul…
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Dear Keegan,
I am working on whole genome bisulfit seq data from 5 different brain tumor types and I would like to investigate what these tumors have in common and what distinguishes them.
Does 'dm…