User: alice.mcgovern

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Posts by alice.mcgovern

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Comment: C: Normalization of RNA-seq data
... Hi, thanks again. Sorry to be annoying but for some reason when I try to run DESeq2 on my files it comes up with an error. My series of events are HISAT2 my fastq files, bams to dge count matrix individually on each HISAT2 file, then perform DEseq2 like you suggested. The error I get it is: To ...
written 8 weeks ago by alice.mcgovern10
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Comment: C: Normalization of RNA-seq data
... Thanks for your response. Basically i have rna seq fastq files on single cells and im not wanting to draw any comparisons on them yet. I'm just hoping to normalize and come up with a table of gene expression. Does edgeR or DESeq2 do that without running differential comparisons? Sorry if this is a ...
written 9 weeks ago by alice.mcgovern10
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Normalization of RNA-seq data
... Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on any of my samples. I can easily run HISAT2 and then sam/bam counts to get a count matrix but I assume this is raw counts? How do I then, at the very least, normalize those counts to account for librar ...
normalization rna-seq written 9 weeks ago by alice.mcgovern10
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Concatenating four Nextseq fastq files
... Hi, Please excuse my naivety but my sequencing was run on NextSeq with single end reads, I have 4 fastq files per sample and therefore need to combine the 4 files. I have been using the concatenate tool and then end up with 4 separate files that are called concatenate datasets on data XX. Which ...
rna-seq written 4 months ago by alice.mcgovern10 • updated 4 months ago by Jennifer Hillman Jackson22k

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