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Recent Replies
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
if the type hasn't been already defined, the type is set as an array of bytes using `OR` and this function: https://github.com/samtools/hts…
Comment: arrange samples in same order in rows and column in R
by
Kevin Blighe
81k
You probably just need: fit <- lmFit(t(mval), var) In your model, you are also attempting to adjust for a lot of covariates- is that…
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
Thank Basti, I already did this, could you please above posted full code? Many thanks,
Comment: Split fastq files
by
GenoMax
115k
> not sure what does the 001 at the end stand for That is a standard part of all illumina files. Ages ago data used to be put in 2M read c…
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
Thank you so much for quick response, but here is the more complete code and I already put CpG as row name and in sampleInfo file (targets2…
Comment: Strange Trimmomatic behavior
by
ctdarwell
• 0
Ah OK so there is no need to remove them?
Comment: Which data files are required to find GWAS summary statistics?
by
4galaxy77
★ 1.7k
Yes, you need all 3 files. Look up 'GWAS in plink' and there is lots of tutorials and help.
Answer: arrange samples in same order in rows and column in R
by
Basti
▴ 330
The issue comes from the presence of your cg....... column so you might put it into rownames to keep the information and then remove the co…
Comment: arrange samples in same order in rows and column in R
by
Kevin Blighe
81k
What is contained in the `var` variable? First, the probe names (first column of betaval2) should be set as rownames, and then you need to…
Comment: Split fastq files
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zeina-younes
• 0
I am sorry i am not a bioinformatician and i am not very familiar with the technical terms that's why my question is not clear. The sample …
Comment: Strange Trimmomatic behavior
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lieven.sterck
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how did you derive this? but indeed, that would make perfect sense and explain the issue here (TAA is likely the remainder of the restrict…
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Jean-Karim Heriche
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> An NVIDIA GPU is necessary only if software can take advantage of it. Not every tool out there is GPU-capable.
Comment: Strange Trimmomatic behavior
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cpad0112
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It's GBS. Look at the cutters.
Comment: Which data files are required to find GWAS summary statistics?
by
Raju
• 0
Do you mean I have to use 3 files or what? can you please elaborate the procedure
Answer: Recent alternative to LalnView
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maxime.policarpo
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Thank for your answers. After checking your propositions, I don't think there are very good alternatives, as annotations must come from gen…
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