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What do you imagine are the first three steps in your class project? Feel free to ask clarifying question in class or using issues..
sr320 updated
5 years ago
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/TheJacksonLaboratory/epihet
Confirm the following…
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For data analysis we need to know library prep details C virginica libraries, enough details so one could reproduce. A major point is whether they are directional.
sr320 updated
6 years ago
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Hi Felix,
I have a large and very fragmented genome that I'm trying to use to analyse wgbs data, which I suspect might be the sole reason I am having so much trouble running bismark. I thought I woul…
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Hi Felix,
I'm a regular user of bismark (actually I had post in seqanswer in the past a few times) and now I have a new set of data that I want to analyze.
As before, let me notice that my reads cam…
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Hi Bismark team,
I'd like to invoke the --no-discordant flag in my alignment, and I'm not sure how to switch the flag. I am getting an error of:
`Unknown option: no-discordant
Please respecify c…
caalo updated
6 years ago
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Hi,
It's definitely not an issue, more a good practice that I'm looking for.
I have a VCF file for some samples, and I would like to use the possibility given by MethylKit to filter the C->T mut…
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Hi Felix,
I am trying to map paired-end reads from Bisulfite sequencing using Bismark.
The genome i used is Zea_mays.AGPv4.dna_rm.fa download from Ensembl, i build index use the commond:
`bismark_…
xiuru updated
6 years ago
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Hi,
I noticed in your paper that you subsetted for DNA methylation probes from the illumina array with the top 1% of variance, as well as the RNA-seq genes with the top 20% of variance across sampl…
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When trying to execute a simple Pamir command,
```
https://github.com/vpc-ccg/pamir/issues
```
I get
```
=============================================
Project Name : pamir_test_4
Working…