updated 4 hours ago by
Jeremy Leipzig
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written 9.9 years ago by
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Comment: Issue with merging in plink and eigensoft.
by
bk11
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> I merged two datasets in plink1.9. It worked, but I did get the error
> "multiple positions seen for variant" and "variants have the same…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
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It worked now, after re-mapping with short-headed FASTA! :) Thanks a lot again for your time.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
svlachavas
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Dear LChart,
thanks a million for your detailed response and explanations !! Some quick updated comments (hopefully not disturb you furth…
Comment: Clustering in single cell
by
Chris
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Just because the articles and tutorials I read, they usually clearly separate which I worry I did something wrong.
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
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> do you think the one or other option (using fasta with shortened
> headers vs. bbmap.sh with trd=t option) would have other advantages or…
Comment: Clustering in single cell
by
bk11
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> However, in my analysis, clusters of each cell types are not clearly
> separate even though I tried different clustering algorithms (louv…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
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0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error:
…
Comment: Clustering in single cell
by
Jean-Karim Heriche
26k
Are you doing the clustering in UMAP space? If so, avoid distance-based clustering because distances are only meaningful locally, i.e dista…
Comment: How to convert data in r?
by
Ram
40k
> tidyr does not make anything tidy at all
I don't get your point. The code does not use tidyr (`%>%` is from `magrittr`) and there is no …
Comment: Unmapped Reads in Kallisto
by
GenoMax
134k
https://www.biostars.org/u/30020/ you can add a solution to this thread. It looks like this poster has a similar issue described in origina…
Comment: Network analysis with cytoscape
by
Chris
▴
200
Thanks xanderpico! That is great resources. There are many bioinformatics tools now which is hard to choose an appropriate one. I found thi…
Comment: Frustrated with DEA results
by
dsull
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Great suggestion on visualizing the data as well as doing DE between variables that you know should result in different gene expression pro…
Answer: Network analysis with cytoscape
by
xanderpico
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Hi Chris.
There are dozens of different directions you could go using Cytoscape. There is not just one analysis path. You mention "tran…
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