User: cxr5298

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cxr52980
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Posts by cxr5298

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Comment: C: One read and One alignment
... In the case where the read aligns twice to the same species I'd consider it a single 'hit' for the species in question. In the case where a read aligns to multiple species it would be something I'd need to investigate further to determine it's origin. I'm more preoccupied with identifying origin of ...
written 13 days ago by cxr52980
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Comment: C: One read and One alignment
... As far as I can tell the alignments appear valid just that there's more than there should be. This phenomenon is across the board whether I'm using `minmap2`, `bowtie2`, `snap`, or `BWA`. I'm not too familiar with CIGAR strings but from what I can tell the alignments all appear to be good. If I want ...
written 13 days ago by cxr52980
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One read and One alignment
... I am working with a data set of ONT MinION metagenome data aligning it against a fasta file where each entry is a different species using a series of aligners (BWA, Bowtie2, SNAP, and Minimap2) to see which aligner yields the best results. However for each alinger I am getting more alignments to the ...
genome next-gen metagenome rna-seq sequencing written 14 days ago by cxr52980 • updated 13 days ago by swbarnes25.5k
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Comment: C: DESeq2 Long Read RNA, normalization, and interpreting expression data
... I'm working with two replicates of an uninfected control, and 8h, 24h, 48h infected samples. Already this is disqualifying in terms of experimental design but due to unfortunate circumstance this is all the data I have to work with for the time being. ...
written 10 months ago by cxr52980
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DESeq2 Long Read RNA, normalization, and interpreting expression data
... Hello, I am working on getting differential gene expression between an infected and uninfected population using direct RNA-seq from a MinION. When loading my values into DESeq and creating a heatmap and MAplot things look strange and I'm not entirely clear on how to interpret it. My MAplot: [Graph ...
R rna-seq sequencing written 10 months ago by cxr52980

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