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. -
Metatranscriptome read mapping yielding a highly left skewed ORF TPM distribution
I'm going to jump right into the problem and put details below for clarification:
What are the possible causes of mapping high quality... -
How to classify chIP-seq reads into gene bins?
Hello everyone!
I am very new to RNA-seq data analysis. Your help on how to accomplish the below task is highly appreciated! I will explain... -
Cuffnorm's FPKM - advisable to perform TPM conversion?
Hi,
I performed a detailed time-course mRNA-seq experiment without any sequencing replicates (the input RNA, however, was a pool of equal... -
Averaging TPM counts among replicates
Hello all,
I calculated TPM counts from an un-normalized HTSeq-count output file for a number of replicates. I am wondering how should... -
Haplotypes in Ensembl cDNA confuse pseudo-alignment
Dear all,
Before I dive into details, my question is whether it is a sound idea to envisage:- an Ensembl "cdna" Fasta file that,
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GFF3 formatting wrong for RSEM?
Hello SEQanswers community,
When I run rsem-prepare-reference with refseq it only captures "tRNA" in my gff3 file. I only realized... -
Pca tpm fpkm
Hi all,
I have expression values in TPM and FPKM from RSEM. Is it correct to perform a PCA direclty on these values or I have to manipulate these... -
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... -
RSEM and cuffdiff
Hi,
I have just re-analysed my data to get TPM rather than FPKM values. I have done this using RSEM.
A google search has... -
The easiest/fastest way to get from BAM to TPM or RPKM
I have already aligned all my RNA-seq samples using tophat2. I've done the differential analysis using htseq-count and edgeR. I would like to get rpkm...
