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Hi
I am using sorted_symmetric_cpg.meth (xyz.meth)files to find HMRs in my dataset using the foll. command:
hmr -p xyz.hmr.params -o xyz.hmr xyz.meth
But I get the foll. error-
gsl: gamma.c:12…
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Hey!
When I analyze the whole human methylome in the bismark, I get a low level of alignment (18%). I checked it in the FastqScreen program, everything is fine with the reads and the quality is also …
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See what it cost to do a wg reseq on the haws samples...
sr320 updated
3 years ago
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Hi,
I am interested in training de novo CpG modified base models with megalodon.
After reading the documentation I have a couple of questions.
As an example, let's say I have two promethION r…
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AWS megatests is now running nicely and we’re trying to set up all (most) nf-core pipelines to run a big dataset. We need to identify a set of public data to run benchmarks for the pipeline.
The id…
ewels updated
3 years ago
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Hi Felix,
first thanks for bismark, i especially love the NOMe-seq option to analyse some new data i have.
So I am trying to align a sample test NOMe-seq data (number of reads is extremely low)…
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This is just an issue to track progress on the idea.
The basic proposal so far is some form of side-channel in a SAM/BAM/CRAM tag which is used in conjunction with the sequence field to characteris…
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I have been trying to align some files to the mouse genome but when I come to the genome preparation step, I get this error (sorry there is so much nonsense):
Bismark Genome Preparation - Step II: …
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I am having issues with MeDIP Bs-Seq, in particular https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1313979
Could please you clarify how to apply BSBOLT for this type of samples? Because I get …
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Hi Simon,
I am trying to use the gemBS pipeline to process some whole human genome bisulfite sequence data that is single-ended. Specifically, I am trying to run the mapping command with non-strand…