User: User 7754

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User 7754170
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United Kingdom
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Posts by User 7754

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Bedtools Error: Type checker found wrong number of fields while tokenizing data
... Hi Pierre, thank you, I have tried that but I still get the same error after doing that to each bed file: cat bed1.corrected.txt bed2.corrected.txt | sort -k1,1 -k2,2n | mergeBed -i stdin > merged.bed ...
written 5 weeks ago by User 7754170
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Comment: C: Bedtools Error: Type checker found wrong number of fields while tokenizing data
... Yes; but shouldn't the sed command get rid of them? ...
written 5 weeks ago by User 7754170
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Bedtools Error: Type checker found wrong number of fields while tokenizing data line.
... Hi, I get an error for having an extra tab but removing the extra tab does not solve the error, has anybody run into this? cat bed1.txt bed2.txt | sort -k1,1 -k2,2n | mergeBed -i stdin > merged.bed Error: Type checker found wrong number of fields while tokenizing data line. Perhaps you h ...
bedtools written 5 weeks ago by User 7754170 • updated 5 weeks ago by Alex Reynolds26k
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GenomicRanges based on indices or more conditions, and add column from match
... I am trying to extract columns based on two conditions from the indices of two overlaps. This is an example: df1 = data.frame(chr=c("chr1", "chr1"), start=c(20,21), stop=c(28,29), value1=c(1,2)) df2 = data.frame(chr=c("chr1", "chr1", "chr1"), start=c(20,22, 28), stop=c(22,24,34), value2=c(3 ...
R genomicranges overlaps written 7 weeks ago by User 7754170
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Get indices from GenomicRanges reduce function
... Hi, Is there any way to extract only the indices of rows that would be reduced by the "reduce" function in GenomicRanges? Thank you ...
R genomicranges reduce written 11 weeks ago by User 7754170 • updated 10 weeks ago by Nicolas Rosewick7.0k
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Comment: C: R reduce across multiple ranges by row
... Yes!! This is exactly what I have been trying to do but kept getting stuck at the reduce part! Brilliant. thanks so much!! Adding scores is simple with this set up! indicesOverlapping = c() scores = c() for (i in 1:nrow(df)) { if (length(queryHits(findOverlaps(df1_GR[i,], df2_G ...
written 12 weeks ago by User 7754170
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Comment: C: R reduce across multiple ranges by row
... Thank you Alex. A.bed B.bed chr1 1 4 chr1 2 5 chr1 3 8 chr1 8 11 chr1 3 14 ...
written 12 weeks ago by User 7754170
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Comment: C: R reduce across multiple ranges by row
... Hi, Thank you for looking into helping. I think R is the most appropriate because of the "GenomicRanges" package, the set up of the problem would be similarly hard with bedtools, unless there is a specific function for this situation. What I am trying to do is merge the overlaps across rows only i ...
written 3 months ago by User 7754170 • updated 12 weeks ago by RamRS19k
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R reduce across multiple ranges by row
... Hi, I have a dataset with two sets of ranges (.df1 and .df2) and I am trying to find a common set of ranges across both simultaneously. Meaning, I would like to reduce the ranges only if they overlap both sequences in a row. df = data.frame(seqnames.df1 = c("chr1", "chr1", "chr1"), start.df1 ...
R genomicranges reduce ranges written 3 months ago by User 7754170 • updated 12 weeks ago by RamRS19k
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R package to annotate and explore effect of biases in RNA Seq
... I was wondering if anybody knows about an R package to do usual annotations of regions (GC content, mappability, etc), in one package instead of bedtools, and to explore the influence of these biases. I realize the first step can be done with bedtools, and possibly analyzing them in a linear model ...
R rna-seq annotation written 3 months ago by User 7754170 • updated 3 months ago by h.mon21k

Latest awards to User 7754

Great Question 9 months ago, created a question with more than 5,000 views. For Plot Genes In R Under A Regional Manhattan Plot
Popular Question 9 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 9 months ago, created a question with more than 1,000 views. For Definition of splicing eQTLs in RNA-Seq and arrays
Popular Question 9 months ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 9 months ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 9 months ago, created a question with more than 1,000 views. For [SOLVED] Trying to apply overlap to each row of a "GRangesList"
Popular Question 14 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 2.2 years ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot
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Popular Question 6.4 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot

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