User: ferbecneu

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ferbecneu0
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Posts by ferbecneu

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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 22 hours ago by ferbecneu0 • updated 9 hours 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 6 days ago by ferbecneu0 • updated 6 days 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 14 days 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 14 days ago by ferbecneu0 • updated 14 days 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 28 days ago by ferbecneu0
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Comment: C: Remove reads from raw fastq
... Thank you, I think that what you answered is just what i need to do but I have a problem. Im working with a fastq file whose reads I read with readDNAstringset and then use thinCounts, however I get this: Error in colSums(x) : 'x' must be numeric. I know that maybe this is too basic but Im starting ...
written 4 weeks ago by ferbecneu0
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Remove reads from raw fastq
... Hi, Im analysing sequencing data and comparing distinct samples, however between two of my conditions I have very different read numbers and that is causing me troubles during the analysis. I would like to remove reads from some of my samples but these reads should be random so that I dont skew my d ...
biostrings shortread written 5 weeks ago by ferbecneu0 • updated 5 weeks ago by Gordon Smyth35k
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FourCseq extraction of fragments
... Hi, I used FourCseq for detection of differences in interactions between two study groups, however after plotDifferences function I would like to know if it is possible to extract the coordinates of the fragments marked as differences between the conditions. Thank you! ...
fourcseq written 5 weeks ago by ferbecneu0
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Comment: C: Retrieving specific sequences from a fastq
... Thank you very much! This was super useful for me :D ...
written 9 weeks ago by ferbecneu0
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Answer: A: Retrieving specific sequences from a fastq
... Thank you Martin, I read the function you said: (filterFastq(files, destinations, ..., filter = FilterRules(), compress=TRUE, yieldSize = 1000000L). However Im starting with bioinformatics and I dont know how to write filter/filterRules to remove the reads that contain the sequence: GCAGTGGGGCGGGTCT ...
written 9 weeks ago by ferbecneu0

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