SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Newbie's Question on align published Chip-Seq data muhe1985 General 0 01-13-2014 06:46 PM
Whole genome alighment and comparision roshanbernard Bioinformatics 0 01-11-2014 12:15 AM
miRNa sequencing and comparision bfantinatti Bioinformatics 2 05-03-2013 04:44 AM
Published RNA seq data honey Bioinformatics 3 12-18-2010 10:56 PM

Reply
 
Thread Tools
Old 10-06-2016, 07:36 AM   #1
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 56
Default 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, sequencing and other downstream analysis to obtain FPKMs was done in a similar way.

As we lack other interesting neuron (type C) RNAseq data, my supervisor advised me to use Published data which obviously is of different protocol and method than ours. Published data on GEO has raw data and already preprocessed information containing the FPKM values of the particular neuronal sample I am interested in.

My question/ concerns:
Unique genes between samples:
1) From each sample, took the genes which satisfy the criteria FPKMS > threshold (along with statistical tests) and obtained sample specific expressed genes. Now I wanted to check how many unique genes exists between samples by excluding the common ones:
Question : Is it OK if I directly compare the genes list between samples??

2) Or Should I have to calculate FPKMs again from rawdata or do any kind of normalization in order to compare between datasets??
priya is offline   Reply With Quote
Reply

Tags
fpkms, normalization, rnasequencing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:23 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO