The unification of mRNA expression value measurements across studies, or the normalization...
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How to Choose Normalization Methods (TPM/RPKM/FPKM) for mRNA Expression
Why do mRNA expression values need to be normalized?
The unification of mRNA expression value measurements across studies, or the normalization...Last edited by Novogene; 09-04-2024, 02:09 PM. -
Why is rpfm of bacterial genomes much higher than eukaryotes
I found the rpkm of my RNA-seq datasets of my bacterial samples much higher than eukaryotes. The rpkm for bacteria is usually 50 or even more than 100.... -
log normalization of RPKM values in voom
I have a question about using voom() on TPM (or RPKM) values. I have TPM values on gene level for 200 samples, and I want to use voom() function to log-normalize... -
views Bowtie2 : aligned result read count not matching with sam Read count
bowtie2 -f -N 1 -p 8 -x REF.fa -1 sample01_1.fasta -2 sample01_2.fasta -S sample01.sam --al sample01_al.fasta --al-conc sample01_alcon.fasta
...Last edited by vinumanikandan; 05-13-2015, 03:05 AM. -
from mean per-base read coverage to RPKM using the Brawand data
Hi:
this involved cross-post
Now I delete the content.
I am sorry. -
how to calculate RPKM from SAM
i am very new to bioinformatics and been trying to learn new things every day.
this time, i need to find out RPKM from a sam file. i mapped... -
how to calculate RPKM from mean per-base read coverage
Hi all:
gene expression level can be presented by mean per-base read coverage(Rz).
It was reported by some researchers that they... -
Normalization / Transformation of DE data with a de novo assembly
Hello,
I have a question regarding transformation and/or normalization as it applies to analysis of differential expression (DE) for a... -
Intrasample exon analysis of RNA-Seq data using RPKM values
Hello SeqAns community,
I have been using Mapsplice and RSEM to analyze RNA-Seq data.
The output of my pipeline are the expected... -
Negative RPKM values by EDGE-pro
Hello,
I am using your EDGE-pro programs for RNA-seq analysis
of bacterial species.
I could run the program, but I got negative... -
Gene length for genes with multiple isoforms
Hi all,
I am trying to determine the most highly expressed genes in some publicly available RNA-seq data, as well as in my own samples.... -
Cytosol/Nucleus ratio from RNA-seq
Hello,
I have RNA-seq data from nucleus and cytosol fractions for a couple of different cell types. I am interested in determining the ratio of... -
FPKM = RPKM for single end reads?
Hi Readers,
I am a computer scientist and I am trying to understand the relationship between RPKM and FPKM. I have read this following... -
Rpkm deg
Hi Everyone,
I am working on a set of samples (generated using Illumina) for differential gene expression between control and treated samples.... -
Calculating RPKM value manually
Hello,
I'm dealing with bacterial RNA-seq data. I would like to show absolute gene expression by calculating RPKM value for every gene....
