User: ta_awwad

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ta_awwad10
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Posts by ta_awwad

<prev • 37 results • page 1 of 4 • next >
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Comment: C: visualize Hi-C .cool file in R
... Thanks much it was really stupid question ... now everything works fine ..thanks once more TA ...
written 9 weeks ago by ta_awwad10
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Comment: C: visualize Hi-C .cool file in R
... I managed to get the interaction matrix .. in my case 878 X 878 .. also I prepared the Granges of the interaction bins (878 Grange) .. now when I am trying to construct HTCexp object gives me the following error message: Error in dimnamesGets(x, value) : invalid dimnames given for “dsyMatrix” o ...
written 9 weeks ago by ta_awwad10
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Comment: C: visualize Hi-C .cool file in R
... Thanks much Nicolas for your quick reply .. it would be great if you implement these functions to be suitable to import several Hi-C output formats Best TA ...
written 9 weeks ago by ta_awwad10
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visualize Hi-C .cool file in R
... Hello everyone, I am really new in visualising Hi-C data. Now I have normalized .cool files and I would like to visiualize it in R using HiTC package .. my .cool files are in the following format: chrom1 start1 end1 chrom2 start2 end2 count balanced chr18 10500000 1060 ...
hitc hi-c written 9 weeks ago by ta_awwad10
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Comment: C: reload IGV exported feature to Gviz
... I figured it out .. jus have to convert this bed format to gff3 and that it. ...
written 9 weeks ago by ta_awwad10
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reload IGV exported feature to Gviz
... Hi everyone, I extracted new annotated gene features from IGV as bed file with this format: chr17 11049086 11051487 YourSeq 999.4911 - 11049086 11051487 . 2 1735,230, 0,2171, chr17 11044924 11051487 YourSeq 995.2607 - 11044924 11051487 . ...
gviz igv written 10 weeks ago by ta_awwad10
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Comment: C: remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
... > seqnames(dds) %in% c("X", "Y")​ RleList of length 52636​ > !seqnames(dds) %in% c("X", "Y") RleList of length 52636 ...
written 11 weeks ago by ta_awwad10
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Comment: C: remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
... thanks much mike, I tried it already but it doesn't seem working as the number of DE genes are still the same as if X and Y genes were not removed! .. I don't know what to do in order to make this correctly. thanks ...
written 11 weeks ago by ta_awwad10
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Comment: A: remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
... Hi Mike, I tried to do the same but it gave me this error message: dds.sub <- dds[ ! seqnames(rowRanges(dds)) %in% c("X","Y"), ] Error in (function (classes, fdef, mtable)  :    unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedRleList"’ ...
written 11 weeks ago by ta_awwad10
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Answer: A: BAM file into R from Illumina
... myBam <-c ("trt_1.bam", "trt_2.bam", "wt_1.bam","wt_2.bam") bamLst <- BamFileList (myBam, yieldSize=2000000) summarizeOverlaps(bamLst,......)   good luck                 ...
written 5 months ago by ta_awwad10

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