User: ta_awwad

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ta_awwad10
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t*******@yahoo.com

Posts by ta_awwad

<prev • 32 results • page 1 of 4 • next >
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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 7 days 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 10 days 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 10 days 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 10 days 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 12 weeks ago by ta_awwad10
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Comment: C: how can I interpret the fold change of Dseq2
... browseVignettes("DESeq2") ...
written 4 months ago by ta_awwad10
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Answer: A: microarray data analysis using limma package
... I think you need  hgu133plus2.db not hgu133aprobe for this array ...
written 7 months ago by ta_awwad10
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QuasR error message
... Hi everybody, I am trying to align my paired end reads in R using QuasR. everything was easy and smooth until the alignment step. I am using the following line for alignment: > proj <- qAlign(sampleFile, genome= genomeFile, splicedAlignment= TRUE, alignmentsDir= "bam", clObj = clObj, paired ...
quasr rna_seq written 7 months ago by ta_awwad10 • updated 7 months ago by Hotz, Hans-Rudolf390
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... thanks a ton .. I did it already ..  ...
written 7 months ago by ta_awwad10
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... Thanks much Robert ... it worked pretty good now...  TA ...
written 7 months ago by ta_awwad10

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