User: Wietje
Wietje • 200
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- 1 year, 11 months ago
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Posts by Wietje
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... Hello fellow Biostars,
I have a Biomart related questions: I downloaded a number of QTL regions from the animalgenome DB and wanted to see which genes overlap with them. I filtered for multiple regions, which all worked fine - however I am unsure which overlap criteria were used and cannot find ano ...
written 19 days ago by
Wietje • 200
• updated
15 days ago by
Emily_Ensembl ♦ 18k
1
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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 months ago by
Wietje • 200
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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 7 months ago by
Wietje • 200
1
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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 7 months ago by
Wietje • 200
0
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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 7 months ago by
Wietje • 200
1
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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 13 months ago by
Wietje • 200
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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 13 months ago by
Wietje • 200
2
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1
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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 13 months ago by
Wietje • 200
0
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1
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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 13 months ago by
Wietje • 200
1
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1
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1.3k
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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 13 months ago by
Wietje • 200
Latest awards to Wietje
Popular Question
6 days ago,
created a question with more than 1,000 views.
For Bedtools intersect QTL animalgenome
Scholar
6 weeks ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For Bedtools intersect QTL animalgenome
Supporter
5 months ago,
voted at least 25 times.
Scholar
13 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
Scholar
16 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
Scholar
23 months ago,
created an answer that has been accepted.
For C: Bedtools intersect QTL animalgenome
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