User: AnonymousEngineer

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Posts by AnonymousEngineer

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Comment: C: TPM-like normalization of time series RNAseq data to minimize dispersion of coun
... I am not sure how DESeq2 fits in. The reads shown here are of the pathogen genes, and I cannot do a differential expression analysis of the pathogen here as reads of pathogen in uninfected control plants are all zeros. Once the pathogen starts to replicate, the reads of the pathogen start to incre ...
written 27 days ago by AnonymousEngineer0
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TPM-like normalization of time series RNAseq data to minimize dispersion of counts within replicates
... Hi everyone, I am working with RNAseq reads from a plant/pathogen culture. The plants are infected with a very small inoculum of pathogen. The number of inoculum delivered successfully to each plant is different, and each plant has different cell mass. At different time points post infection RNA i ...
time-series normalization tpm rna-seq written 27 days ago by AnonymousEngineer0
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DESeq2: (1) Comparing multiple groups using a for loop & (2) normalization of time series data with housekeeping gene counts
... Hi Everyone: I am trying to analyze a set of RNAseq data using DESeq2 to do a GO enrichment analysis. In my dataset have 8 groups. The groups are `cond_09 cond_10 cond_11 cond_12 cond_13 cond_14 cond_15 cond_16` with 3 replicates`A, B & C`' for each group. The columns in my input TSV file are ...
rnaseq R deseq2 deseq written 7 months ago by AnonymousEngineer0 • updated 7 months ago by ATpoint34k
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Comment: A: Can I assemble a bunch of contigs of a bacterial genome to get the full genome s
... Thank you for the explanations, I appreciate it. I will try contacting the authors for the original sequencing reads are available. What would be a good program of choice when it comes to assembly? On another note, can the sequencing coverage and / or quality be improved by repeating the sequencing ...
written 12 months ago by AnonymousEngineer0
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Can I assemble a bunch of contigs of a bacterial genome to get the full genome sequence?
... Hi everyone, I am fairly new to bioinformatics and I am trying to wrap my head around genome sequencing and assembly. I need to analyze this genome of this bacteria called Shewanella benthica KT99 to predict genes encoded in its genome. However, the reported assembly level of the genome is in cont ...
assembly sequence alignment sequencing written 12 months ago by AnonymousEngineer0

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