User: ta_awwad

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ta_awwad10
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10
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New User
Location:
Frankfurt am Main
Last seen:
4 months, 1 week ago
Joined:
2 years, 10 months ago
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t*******@yahoo.com

Posts by ta_awwad

<prev • 41 results • page 2 of 5 • next >
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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 12 months 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 12 months 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 12 months 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 15 months ago by ta_awwad10
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Comment: C: how can I interpret the fold change of Dseq2
... browseVignettes("DESeq2") ...
written 16 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 19 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 19 months ago by ta_awwad10 • updated 19 months ago by Hotz, Hans-Rudolf400
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... thanks a ton .. I did it already ..  ...
written 19 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 19 months ago by ta_awwad10
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... Hi Tiphaine, I already tried chromHMM_RoadMap to generate chromHMM15. there is no coloured features were shown only blue bar. here is my bed file format: chr1 75421401 75421600 TssBiv chr1 75421601 75421800 TssBiv chr1 75421801 75422000 TssBiv chr1 75422001 7542 ...
written 19 months ago by ta_awwad10

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Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2: collapseReplicates error

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