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User: Wietje

gravatar for Wietje
Wietje • 210
Reputation:
210
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Trusted
Location:
Germany
Last seen:
4 days, 1 hour ago
Joined:
2 years, 8 months ago
Email:
n****@fbn-dummerstorf.de

Posts by Wietje

<prev • 41 results • page 1 of 5 • next >
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Answer: A: How to show an attribute next to the label in Cytoscape
... I suppose the easiest way to display gene symbol + gene ID together is to prepare an input table that has 1 extra column with both IDs next to each other. Load this table into Cytoscape, go to "Style" and choose "Label", click on the three little dots and select the column of your own making. ...
written 4 months ago by Wietje • 210
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Ensembl Biomart overlap QTL regions and genes
... 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 ...
genome ensembl biomart written 10 months ago by Wietje • 210 • updated 10 months ago by Emily_Ensembl ♦ 20k
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Comment: C: Co-expression network using Cytoscape
... 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 16 months ago by Wietje • 210
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Comment: C: Co-expression network using Cytoscape
... 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 16 months ago by Wietje • 210
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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 16 months ago by Wietje • 210
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Answer: A: Co-expression network using Cytoscape
... 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 16 months ago by Wietje • 210
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Answer: A: Runs of homozygosity calculation
... 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 22 months ago by Wietje • 210
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Answer: A: Decreased base quality at start of RNA seq reads
... 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 22 months ago by Wietje • 210
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Answer: A: How to convert PLINK file (map, ped) to haplotype file for XPEHH application
... 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 22 months ago by Wietje • 210
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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 23 months ago by Wietje • 210

Latest awards to Wietje

Popular Question 3 months ago, created a question with more than 1,000 views. For imputation and changing genotypes in Beagle and FImpute
Popular Question 8 months ago, created a question with more than 1,000 views. For Bedtools intersect QTL animalgenome
Popular Question 9 months ago, created a question with more than 1,000 views. For Bedtools intersect QTL animalgenome
Scholar 10 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Popular Question 12 months ago, created a question with more than 1,000 views. For Bedtools intersect QTL animalgenome
Supporter 14 months ago, voted at least 25 times.
Scholar 23 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 2.1 years ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 2.7 years ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
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