User: Wietje

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Wietje150
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Posts by Wietje

<prev • 35 results • page 1 of 4 • next >
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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 4 months ago by Wietje150
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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 4 months ago by Wietje150
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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 4 months ago by Wietje150
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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 5 months ago by Wietje150
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Answer: A: Read MAP and PED files in PLINK
... Could you tell us what error message you got exactly and what your code was? That would help with debugging... ...
written 5 months ago by Wietje150
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Answer: A: How to create heatmaps only with DE genes in edgeR
... 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 5 months ago by Wietje150
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Answer: A: Sort the 'score' value for each aligned sequence
... Assuming your file is loaded as a dataframe, youcould give this a try (how exactly did you use order() on your data? could you provide the actual code you used?): x= df[order(df[,"score"],decreasing = TRUE), ] This should sort your dataframe in decreasing order based on the score (make sure "s ...
written 5 months ago by Wietje150
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Answer: A: Calculate the genotype frequency
... You might want to try PLINK which allows you to read in a VCF file (--vcf [INPUTFILE]), select only a few individuals (--keep [FILE]) and then get genotype frequencies with --freqx (with aditional option --nonfounders if you want to have it for all individuals in your list) or allele frequencis with ...
written 5 months ago by Wietje150
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Comment: C: FeatureCounts fails to count fragments instead of reads
... Not necessarily, there are also unpaired reads in the file, but the multialigning ones happen to be paired most of the time as far as I can see. ...
written 6 months ago by Wietje150
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Comment: C: FeatureCounts fails to count fragments instead of reads
... Yes, I only filtered for "listed first in the file", something like this: samtools view -h input.bam | awk -F"\t" '{if(NR>3319 && NR<3369 && $22!="NH:i:1" || NR>3319 && NR<3369 && $23!="NH:i:1"); else print $0}'|samtools view -bS - > new.bam The ...
written 6 months ago by Wietje150

Latest awards to Wietje

Scholar 5 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 7 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 15 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome

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