User: ferbecneu

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ferbecneu0
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Posts by ferbecneu

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Comment: C: Change sign from Granges scores to visualize negative strand data
... It was the second scenario. Thank you very much! ...
written 9 weeks ago by ferbecneu0
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Comment: C: Change sign from Granges scores to visualize negative strand data
... It was the second scenario. Thank you very much! ...
written 9 weeks ago by ferbecneu0
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Change sign from Granges scores to visualize negative strand data
... Hello I wish to add minus signs in my granges scores. These scores come from a Gro-seq bigwig and they are counts from the negative strand however they come as positive values. I want to make them negative so that I can visualize the signal together with positive strand tracks in the genome browser. ...
rtracklayer granges written 9 weeks ago by ferbecneu0 • updated 9 weeks ago by James W. MacDonald49k
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Comment: C: fourCseq - error getZscores
... Hi Wolfgang, Im getting a similar error: Error in getZScores(data, removeZeros= TRUEminCount = 30, fitFun = distFitMonotoneSymmetric) : Failed to estimate the parameters of the Variance stabilizing transformation However I only get it while making certain comparisons between my experimental grou ...
written 3 months ago by ferbecneu0
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Comment: C: Visualizing 4c-seq as arc
... Thank you! Im a begginer with bioinformatics and genomic data analysis so I will be very grateful If you give me a little help. I have my interaction data in bedGraph and Wig format which I think are not accepted by the function makeGenomicInteractionsFromFile since this files only have the inform ...
written 4 months ago by ferbecneu0
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Visualizing 4c-seq as arc
... Hi, I would like to know if genomicinteractions package can be used with 4c-seq data. Or which other tools can I use to create a bedpe for further visualization as arc in WUSTL epigenome browser. Thank you! ...
gviz genomicinteractions interactionset written 4 months ago by ferbecneu0 • updated 4 months ago by liz.ingsimmons120
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Subset bam file in R
... Hi, I want to subset alignments in chromosome 7 from a BAM file and write a new BAM of only chr7 alignments. I made this: seq3<-"HF6_1_1fragmm9.bam" seq3reads<-readGAlignments(seq3) seq3chr7 <- seq3reads[seqnames(seq3reads) == 'chr7'] But I dont know how can I export seq3chr7 as a BAM fi ...
genomicranges rsamtools genomicalignments written 4 months ago by ferbecneu0 • updated 4 months ago by Michael Lawrence10k
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Comment: C: How to convert bedgraph to wig
... Thank you very much! It was very helpful! ...
written 4 months ago by ferbecneu0
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How to convert bedgraph to wig
... Hi, i would like to convert a bedgraph document to wig format for downstream data analyisis for which I require a wig file.  I have it in the format: track name=CD6_1_RPMs description="read per million" type=bedGraph chr1 3005880 3006265 0.788085378200589 chr1 3006269 30 ...
rtracklayer genomicranges written 4 months ago by ferbecneu0 • updated 4 months ago by Michael Lawrence10k
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Answer: A: FourCSeq - how to write tables with the results
... Hi Felix I tried doing what you advised with combinedData <- cbind(as.data.frame(rowRanges(fcf)), results)  and also with mcols(frags) <- cbind(mcols(frags), DataFrame(zScore))  but I get the error: Error in DataFrame(..., check.names = FALSE) :    different row counts implied by arguments ...
written 5 months ago by ferbecneu0

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