User: dina.hesham139

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Posts by dina.hesham139

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Comment: C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
... I will try Thank you! ...
written 6 weeks ago by dina.hesham139120
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Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
... Hi, I 'm trying to analyze my kallisto data with IsoformSwitchAnalyzeR but I get this error when I use the importRdata function, I get this error: > aSwitchList <- importRdata( + isoformCountMatrix = mySwitchList$counts, + isoformRepExpression = mySwitchList$abundance, + ...
isoformswitchanalyzer rna-seq written 6 weeks ago by dina.hesham139120 • updated 1 day ago by liuwei0
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Comment: C: Alternative splicing analysis following kallisto?
... Hi kristoffer, I 'm trying to analyze my kallisto data with IsoformSwitchAnalyzeR but I get this error when I use the importRdata function, I get this error: > aSwitchList <- importRdata( + isoformCountMatrix = mySwitchList$counts, + isoformRepExpression = mySwitchList$abund ...
written 6 weeks ago by dina.hesham139120
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Astalavista landscape AS gtf file output
... Hi, Have anyone tried Astalavista for alternative splicing analysis? If yes, how do I proceed after obtaining the LandscapeAS.gtf file? Thanks in advance! ...
astalavista rna-seq written 11 months ago by dina.hesham139120
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Comment: C: ASPLI (RNAseq AS) R package error
... bam files ranges 6-8gb. I analyze 2 at a time I used windows at first of 8gb RAM. Then I analyzed the data using a macbook pro 256, 2.3 GHz, 8 GB RAM. Also, gave me a memory error! ...
written 11 months ago by dina.hesham139120
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ASPLI (RNAseq AS) R package error
... Hi, I'm using ASPLI (An integrative R package for analysing alternative splicing) to study RNAseq data. Whenever I try to load the bam files I get this error: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (167772160 bytes) file: WT_C1.bam index: NA Any ...
R rna-seq aspli written 11 months ago by dina.hesham139120 • updated 11 months ago by RamRS22k
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Comment: C: Alternative splicing analysis following kallisto?
... Thanks alot Istvan ! What other pipeline would you recommend for studing alternative splicing? esp. for rice and in my case I have a condition that doesn't have a replicate (i.e. I can't use rMATS for example!)? ...
written 14 months ago by dina.hesham139120
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AStalavista for rice alternative splicing analysis?
... Hi, Did anyone try AStalavista for alternative splicing analysis, esp.for rice RNASeq data? Does it manage to work if one of the conditions doesn't have a replicate? (a major drawback to rMATS!!) Is there a tutorial to follow? Thanks in advance! ...
rna-seq alternative splicing written 14 months ago by dina.hesham139120
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Alternative splicing analysis following kallisto?
... Hi, I used Kallisto for analyzing Rice RNAseq data, is there any tool that I can use to study alternative splicing following kallisto, a tool that doesn't require bam files and supports Rice genome? Thanks in advance! ...
kallisto rna-seq alternative splicing written 14 months ago by dina.hesham139120 • updated 14 months ago by kristoffer.vittingseerup1.8k
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Comment: C: RNAseq Rice: multiple condition testing and annotation
... Thank you! I will give it a try! ...
written 15 months ago by dina.hesham139120

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