Questions tagged [rsem]

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1answer
94 views

How to calculate fold change in gene expression from RSEM (RNAseq)

I have gene expression data from RNAseq, specifically: log2(x+1) transformed RSEM normalized counts. How can I convert these data from multiple samples to determine fold change in gene expression?
2
votes
2answers
559 views

STAR quantMode vs RSEM vs Kallisto

I recently discovered this Snakemake pipeline for RNASeq that uses STAR's quantMode to quantify gene expression for DESeq2 differential expression analysis. In the past I've always seen the workflow ...
1
vote
1answer
31 views

Why I am getting different gene lengths for the same genes in different samples with rsem-calculate-expression?

I am running the STAR-RSEM pipeline, I have a simple shell script(*), which I use to loop over fasta files corresponding to different samples. From the output, I am ...
9
votes
2answers
788 views

Duplicate genes with RSEM counts: Which one to choose?

I have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice. ...
8
votes
1answer
2k views

How to apply upperquartile normalization on RSEM expected counts?

I see that TCGA RNASeq V2 RSEM data is normalized with upper-quartile normalization. After doing Quantification with RSEM with the samples I have, I got "genes.results" as output which has gene id, ...
6
votes
1answer
265 views

Is it possible to calculate p-values for fold changes of single replicate RNA-seq samples?

I'm thinking that this isn't actually possible, but I'd like to check before I write it off. I have RNA-seq data from cells under three different conditions, there are no replicates for any of the ...
6
votes
2answers
447 views

Missing genes and normalisation of RSEM output using EBSeq

Without going into too much background, I just joined up with a lab as a bioinformatics intern while I'm completing my masters degree in the field. The lab has data from an RNA-seq they outsourced, ...