User: Wietje
Wietje • 170
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Posts by Wietje
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... It's like I said, you would need to change from this matrix structure (wide format) to long format, which can easily be done with R. [Stackoverflow][1] and the [R-cookbook][2] both have helpful posts on how to do this. If the answer on top is a solution to your initial problem, please consider upvot ...
written 7 weeks ago by
Wietje • 170
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... when you upload network information you can chose what the different columns represent and how they are separated and if there is a header or not. Cytoscape offers very detailed and helpful tutorials to get you started - you might want to considering going through [this][1] one.
I am not quite sur ...
written 8 weeks ago by
Wietje • 170
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Comment:
C: RNA-seq mapping rate
... It might be interesting to know which species you're working with since a mapping rate of 40% would seem very low in human or mice but not in another species that is less well annotated. And the tissue you are working with obviously also plays into that evaluation. ...
written 8 weeks ago by
Wietje • 170
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... Your input data can just be in .txt format and you basically just need to include the mRNA and lncRNA (so one identifier in each column) and in a third column the correlation value. That's enough to build a simple network in Cytoscape. Just import the file with FILE -> IMPORT -> NETWORK -> ...
written 8 weeks ago by
Wietje • 170
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... PLINK assumes that you have a ped and map file when you use --file (same prefix, different file ending); did you try to specify for VCF format with --vcf? PLINK would otherwise also allow you to convert your VCF to ped and map with a --recode option. Does this help you along? ...
written 7 months ago by
Wietje • 170
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... Take a look at [this post][1] and the answers that have been suggested - maybe this is of some help to you.
[1]: http://seqanswers.com/forums/showthread.php?t=61936 ...
written 7 months ago by
Wietje • 170
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... To define haplotypes you will need to phase your data (e.g. with Beagle or Shapeit); the conversion to 0-1 format can be accomplished in PLINK (--recode 01). you might want to take a closer look at the PLINK [manual][1] and the various options.
And maybe check whether your question has popped up ...
written 7 months ago by
Wietje • 170
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Comment:
C: Read MAP and PED files in PLINK
... Could you provide an excerpt from the map file? And most importantly - in your directory screenshot the PED and MAP file are listed as text documents, so apparently something went wrong when saving the file. Did you export directly from Excel? I often exported to Notepad (text editor) first with cop ...
written 8 months ago by
Wietje • 170
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... Could you tell us what error message you got exactly and what your code was? That would help with debugging... ...
written 8 months ago by
Wietje • 170
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... Have you tried to build a subset with those 20 genes? I assume you have one gene per row in which case you should take a look at this post:
[https://www.biostars.org/p/186063/][1]
[1]: https://www.biostars.org/p/186063/
From there on the process should be exactly the same. Does this help you? ...
written 8 months ago by
Wietje • 170
Latest awards to Wietje
Scholar
8 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
Scholar
11 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
Scholar
18 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
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