User: Wietje
Wietje • 150
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Posts by Wietje
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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 4 months ago by
Wietje • 150
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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 4 months ago by
Wietje • 150
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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 4 months ago by
Wietje • 150
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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
Wietje • 150
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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 5 months ago by
Wietje • 150
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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 5 months ago by
Wietje • 150
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... 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
Wietje • 150
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... 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
Wietje • 150
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... 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
Wietje • 150
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... 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
Wietje • 150
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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