User: dorarinyo88

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dorarinyo8820
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Posts by dorarinyo88

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Validate the VCF file by freebayes
... Hello there, Thanks for the reply. The "Mpileup" means the output of samtools mpileup. I'm positive with the result produce by samtools pileup. I just wanted to know that the file produce by Freebayes VCF file is more likely to be similar with the samtools mpileup VCF file. Is there anyway to va ...
written 11 weeks ago by dorarinyo8820
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Validate the VCF file by freebayes
... Hello, I had run two types of variant calling using Freebayes and Mpileup with several individuals. While calling the variants using Freebayes, one of the individuals already successfully converted into VCF file which is larger file size compare to the others. So, how am I going to validate it wheth ...
next-gen snp written 11 weeks ago by dorarinyo8820 • updated 28 days ago by Biostar ♦♦ 20
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Comment: C: Compare two genotype data frame and calculate percentage of differences
... I was wondering that if I can add one more condition that whenever there is "?", the command skip through it and does not include in the final count. For example, the row consists of "?" with NF of 5 instead I just counted 4. I know just to add a counter, but I don't know where I should make the cha ...
written 4 months ago by dorarinyo8820 • updated 4 months ago by zx87546.5k
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Comment: C: Compare two genotype data frame and calculate percentage of differences
... During this step it gives me this error. Is it somehow when comparing different factors in the files. tmp <- set1[,2:ncol(set1)] == set2[,2:ncol(set2)] Error in Ops.factor(left, right) : level sets of factors are different. ...
written 4 months ago by dorarinyo8820
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Comment: C: Compare two genotype data frame and calculate percentage of differences
... Thanks it works. It is a great help ...
written 4 months ago by dorarinyo8820
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(Closed) Compare two genotype data frame and calculate percentage of differences
... Hello there, I have 2 files with the same header and same 1st column, I would like to compare rows by rows and calculate the percentage of matches of the genotype. Somehow I try to transpose it to compare column by column by using the function compare in r, I even try use awk to do the comparing, so ...
R linux awk written 4 months ago by dorarinyo8820
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Compare two genotype data frame and calculate percentage of differences
... Hello there, I have 2 files with the same header and same 1st column, I would like to compare rows by rows and calculate the percentage of matches of the genotype. Somehow I try to transpose it to compare column by column by using the function compare in r, I even try use awk to do the comparing, so ...
R linux awk written 4 months ago by dorarinyo8820 • updated 4 months ago by Pierre Lindenbaum116k

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