User: sum31278

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sum312780
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Posts by sum31278

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Comment: C: Differential expression analysis for STAR-aligned RNA-Seq data
... I am using 'Rsubread' version 1.12.6. ...
written 2.6 years ago by sum312780
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Comment: C: Differential expression analysis for STAR-aligned RNA-Seq data
... Hi Wei Shi, I did use featureCounts as follows: > fc <- featureCounts(files= filenames, annot.ext = "Rnor_6.0.84.gtf", isGTFAnnotationFile =TRUE, GTF.featureType = "exon", GTF.attrType = "gene_id", chrAliases=NULL, useMetaFeatures = TRUE, allowMultiOverlap = FALSE, isPairedEnd=TRUE, require ...
written 2.6 years ago by sum312780
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Comment: C: Differential expression analysis for STAR-aligned RNA-Seq data
... Hi Michael,  I am following the workflow as suggested. When I ran the following command, after sometime the system responded with a warning stating it is low on memory and R should be closed. se <- summarizeOverlaps(features=ebg, reads = bamfiles, mode = "Union", singleEnd = FALSE, ignore.str ...
written 2.6 years ago by sum312780
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Comment: C: Differential expression analysis for STAR-aligned RNA-Seq data
... Thank you Michael Love for the reply. However, I did not understand how the order of the file would make the difference. ...
written 2.6 years ago by sum312780
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Differential expression analysis for STAR-aligned RNA-Seq data
... I have done alignment for paired-end RNA-Seq data using STAR. I now want to do differential expression analysis using the following workflow: http://www.bioconductor.org/help/workflows/rnaseqGene/ I have a few questions before I proceed.   1) I have generated both Unsorted and SortedByCoordinate ...
rnaseq deseq2 star written 2.7 years ago by sum312780 • updated 2.7 years ago by Michael Love22k

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