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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
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0
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
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30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
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bk11
★
2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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GenoMax
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Please include a link when you are recommending a tool. There can be programs with similar names.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Ram
43k
Simple:
```r
data <- lapply(files, read_tsv)
data <- Reduce(merge, data) # or Reduce(full_join, data)
```
<a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
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ATpoint
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments
…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
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1.7k
Hi,
Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
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i.sudbery
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Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value.
https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
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sapuizait
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
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bk11
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I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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GenoMax
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> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes?
Reads are likely aligning in regions wh…
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