What is the best approach to normalize exon read counts between samples ?
Hello I'm trying to calculate the read count for each exon in one of my genes for 3 affected patients and 3 unaffected patients from my RNA-seq data . I'm trying to find the best way to normalize these read counts to factor in variance in exon read depth and exon length between patients. Would calculating the tpm or fpkm be the best way to do this so I can compare read counts of each exon between
• 1,552 views
•
link
written
by
Adeler001 •
1 answer
There are packages such as DEXSeq specifically for performing exon-level differential expression analysis: https://bioconductor.org/packages/release/bioc/html/DEXSeq.html
Log in to answer this question.
More posts like this
-
Is it possible to convert 3 prime sequencing read counts into TPMs?
written by Mat •
-
Blog: How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression
written by Novogene •
-
RNA-seq normalization methods between samples
written by chansik •
-
compare expression for 1 gene between more than 2 samples
written by Sara
-
deseq2 read counts vs featurecount read counts
written by Adeler001 •
-
How to classify chIP-seq reads into gene bins?
written by Zee_S
-
Formula to calculate FPKM
written by vinayjrao
-
Normalise read counts between two bam files
written by nanana
-
Calculate TPM from cuffnorm count data
written by galozs •
-
Detection of CNVs
written by nkausthu •
