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I have set `make_snps = True` at the `extract` step in the `config` file as below to get SNP output. Although it runs the process and generates the [specified](http://statgen.cnag.cat/gemBS/UserGuide/…
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Fang Lab,
Unfortunately the singularity installation option wasn't working for for our campus cluster or my lab machines. As such, I had to set up a conda environment on our cluster and attemptted …
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I am trying to use estimateCellCounts2 on an RGset of 450k probes, however, I am getting the error: Error in match.arg(referencePlatform): 'arg' should be “IlluminaHumanMethylationEPIC”. However, my …
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Hello,
I've been running the most recent Dockerized version of Trinotate. I completed steps 2, 3, and 4 as seen in https://github.com/Trinotate/Trinotate/wiki/Software-installation-and-data-require…
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hello! thanks for building this tools! I met some problems when I try to deal with my WGBS data.
I tried to run wg-blimp from config file, but I went some error, it cannot be run successfully.
t…
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[tomte](https://github.com/genomic-medicine-sweden/tomte) and other pipelines including [DROP](https://github.com/gagneurlab/drop) components will produce shortlists of aberrant expression (`OUTRIDER`…
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I have been looking into using the RNA-seq data but have some questions on the gene annotations for the V2-RNA-seq data that I get from running your GDC-prepare-function.
How do the 21022 genes tha…
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Hi, Illumina discontinued the earlier version of the EPIC array. Can you suggest a way to use RnBeads with EPIC v2.0 data?
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Dear Team,
I am calculating Partition heritability , but I am getting error of "parsing annotation error". Can you please help me with this? Here is my command:
GWAS trait: PASS.Bipolar_Disorder_AL…
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* **PTHR ID & PTN node:**
PTN000473397 & PTN004463688 (PTHR14614)
* **Sequences with problematic annotation (ID + gene/protein name):**
e.g. fly CG17219 (FBgn0031494/Q9VQK8)
* **Type of Issu…
sjm41 updated
2 months ago