Go Back   SEQanswers > Introductions
Similar Threads
Thread Thread Starter Forum Replies Last Post
Count C versus read length EpiBrass Bioinformatics 1 01-28-2014 12:58 AM
Correlation FPKM and RPKM wynstep RNA Sequencing 10 01-17-2014 04:11 AM
fastq.gz stats READ-COUNT BASE-COUNT jgibbons1 Bioinformatics 9 10-30-2013 05:24 AM
How do you get the gene length that htseq-count is using? jebe RNA Sequencing 0 03-07-2013 08:37 AM
the gene fpkm and isoform fpkm are zero with Cufflink ??? fulxie RNA Sequencing 5 05-10-2012 12:41 AM

Thread Tools
Old 04-02-2014, 02:24 AM   #1
Junior Member
Location: Germany

Join Date: Apr 2014
Posts: 1
Default FPKM despite no length ~ count correlation?

Hi all,

I am working with Illumina HiSeq paired-end reads mapped with Bowtie2 to a bacterial reference genome in 3 biological replicates. By now, I pursued two strategies to quantify the mapped reads per gene.
(1) Used HTSeq (union- mode) to get read counts followed by TMM normalisation
(2) Used Cufflinks to calculate FPKMs (with and w.o. length correction)

Since I have only biological replicates but no different treatments/conditions my aim is to make more general statements about gene expression (like mean values) under this one condition and not necessarily assessing differential expression between the biol. replicates.
I'm new in the field of RNA-seq but hardly realised that there are lots of tools but few standards. However, consensus seems to be that comparing gene expression within one genome requires normalisation by gene length and comparisons between same genes but different samples normalization by library size.
But as I tested correlation between HTSeq counts and gene length I found no correlation at all.

(A) is it ok to normalise for length despite of a missing count vs. gene_length correlation
(B) What would you recommend for a quantification/ normalisation strategy in my specific case?
mj21 is offline   Reply With Quote

cufflinks, fpkm, htseq count, normalisation, rna-seq

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 07:41 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO