Questions tagged [rsem]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
0 answers
249 views

SLURM script for running RSEM star fails

If you have worked on cluster with submitting jobs, please help me in resolving the following error. I am running rsem pipeline to generate star index. In principal STAR requires more than 30G of RAM ...
Angelo's user avatar
  • 237
2 votes
1 answer
584 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?
Sylvia Rodriguez's user avatar
2 votes
2 answers
5k 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 ...
Tomas Bencomo's user avatar
1 vote
1 answer
255 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 ...
haci's user avatar
  • 4,092
9 votes
2 answers
2k 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. ...
stack_learner's user avatar
10 votes
1 answer
5k 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, ...
stack_learner's user avatar
6 votes
1 answer
853 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 ...
J0HN_TIT0R's user avatar
7 votes
2 answers
556 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, ...
J0HN_TIT0R's user avatar