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From RNA-seq raw counts to normalized data
I have several RNA-seq datasets. Some of them provide RNA-seq raw counts, some provide FPKM, RPKM and some have transcripts per million (TPM) data. Non... -
Deseq2 normalization between and among the samples
Hello everyone,
I would like to know how the normalization of DeSeq2 works among the replicates of the same sample and between different treatment... -
Combining multiple bams without losing library size information?
Hello all,
I have beeing searching the internet but I have not found what I need to know. Let's say that I have 3 or more bam files representing... -
1/5 Nextera Flex number of cycles
Hi,
We are about to start a fairly large experiment with the Nextera Flex kit in a very limited time. After some testing and reading experiences... -
Normalization from different NGS runs
Hello community, I would certainly appreciate some help here. Many thanks in advance.
I have been looking around about this subject and everything... -
featureCounts - does it normalize by gene length?
Hello,
I'm starting to analyze RNA seq data, and I was hoping you can please help me clear something up
I am using FASTQ groomer,... -
some variants disappear after bcftools norm
Hello,
I noticed that when performing left-normalization on my vcf file (as suggested by Annovar at http://annovar.openbioinformatics.... -
FeatureCounts Normalization
Hi,
I've been using FeatureCounts on differentially accessible regions between multiple atac-seq samples to get the reads per region in... -
how to normalize reads in metatranscriptomes?
[Note: I posted this question on Biostars as well https://www.biostars.org/p/295807/]
I am wondering if anyone here is familiar with this... -
Question about library normalization methods
Hi all,
I am looking for a bead based library normalization method as an alternative to the library normalization in the NexteraXT kit.... -
2 treatments and 1 control, a three way normalization for cufflink output
I have 2 treatment samples -A and B and they both need to normalized to control sample before I compare between A and B itself. How do I do this with... -
comparision with Published RNA-seq
Hi,
I have RNA seq data which contain information about mRNA levels of two neuronal types (Eg: type A , type B).
Experiments,library preparation,... -
TPM and FPLM problem?
Hi
I have used Illumina hiseq 2000 to sequence two samples (two organs of a plant) without replication. I know that without replication I can not...Last edited by Ahmadiut; 06-24-2016, 04:08 AM. -
SequalPrep normalization plates and low amount of starting material
Hi,
I have been looking into Invitrogen's (ThermoFisher Scientific) SequalPrep normalization plates for a quick way to clean and normalize... -
Up to date ERCC spike ins RNA seq analysis
Hello everybody,
I'm expecting to get my ERCC spiked RNA seq sequencing files soon.
Therefore i would like to find out what's the...
