User: dina.hesham139

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Posts by dina.hesham139

<prev • 46 results • page 1 of 5 • next >
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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 7 months ago by dina.hesham139100
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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 7 months ago by dina.hesham139100
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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 7 months ago by dina.hesham139100 • updated 7 months ago by RamRS20k
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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 9 months ago by dina.hesham139100
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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 9 months ago by dina.hesham139100
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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 10 months ago by dina.hesham139100 • updated 10 months ago by kristoffer.vittingseerup1.4k
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Comment: C: RNAseq Rice: multiple condition testing and annotation
... Thank you! I will give it a try! ...
written 11 months ago by dina.hesham139100
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RNAseq Rice: multiple condition testing and annotation
... Hello, I'm working on Rice rnaseq data. Kallisto was used for the pseudo-alignment. I have to questions: 1- I have 6 conditions 2 replicates each (12 samples in total), how can I do multiple condition testing to get the differential expressed genes? I tried sleuth and deseq2 but I couldn't do all ...
rice rna-seq written 11 months ago by dina.hesham139100 • updated 11 months ago by h.mon23k
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Comment: C: "makeTxDbFromGFF" error ?!
... I re-installed all the packages and the error is not yet resolved! ...
written 14 months ago by dina.hesham139100
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"makeTxDbFromGFF" error ?!
... Hey, I'm using deseq2 after kallisto to analyze rice data. I'm using an ensembl gtf and I want to create a txdb. I used this one: txdb2 <- makeTxDbFromGFF(file="C:/Users/Dee/Desktop/Thesis_rice/Oryza_sativa.IRGSP-1.0.37.gtf", format=("gtf"), dataSource=paste("ftp://ftp.ensemblgenomes.org/pub ...
tximport rna-seq written 14 months ago by dina.hesham139100 • updated 14 months ago by Bastien Hervé3.3k

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