Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • sindrle
    replied
    Originally posted by Gordon Smyth View Post
    An appropriate measure of gene length must be input to rpkm(). Computing gene length is a job for the read count software rather than for the differential expression software because the appropriate measure of gene length depends on the way the reads have been counted.

    I use subread and featureCounts:

    featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.


    to count reads. For most RNA-seq analyses, I count reads that overlap any exon for each gene, so the appropriate measure of gene length is the total exon length. Gene length is returned as part of the output from featureCounts.
    I have used HTSeq for counting, I guess I can run featureCounts on one sample, just to get the gene lengths from my UCSC GTF file.

    Then import the lengths to edgeR/DEseq fpkm()

    Or am I missing some points here?

    Leave a comment:


  • sindrle
    replied
    Thanks!

    Is there a difference in choosing CPM/logCPM/FPKM to represent gene expression level if I want to correlate the expression of one gene against i.e. body weight?

    Or the change in gene expression of one gene against change in body weight etc.

    Leave a comment:


  • Gordon Smyth
    replied
    An appropriate measure of gene length must be input to rpkm(). Computing gene length is a job for the read count software rather than for the differential expression software because the appropriate measure of gene length depends on the way the reads have been counted.

    I use subread and featureCounts:

    featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.


    to count reads. For most RNA-seq analyses, I count reads that overlap any exon for each gene, so the appropriate measure of gene length is the total exon length. Gene length is returned as part of the output from featureCounts.

    Leave a comment:


  • sindrle
    replied
    Im wondering the exact same thing..

    Leave a comment:


  • narges
    replied
    Originally posted by Gordon Smyth View Post
    The version of edgeR on the Bioconductor developmental repository has a function rpkm().
    Thank you but can I ask how does this function calculate the gene length? Because my problem is that I do not know how to get the gene length to calculate the RPKM values. The gtf file I have used is the hg19 latest version from UCSC genome browser. I can do something like this: endposition - startpositoin+1. But there are different transcripts for each gene. which of these transcripts should be the as the source for the gene length? the average? the longest?

    Leave a comment:


  • Gordon Smyth
    replied
    Originally posted by ThePresident View Post
    Is it v3.08?
    No, the *development* repository:

    Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data.

    Leave a comment:


  • ThePresident
    replied
    Originally posted by Gordon Smyth View Post
    The version of edgeR on the Bioconductor developmental repository has a function rpkm().
    Is it v3.08?

    Leave a comment:


  • Gordon Smyth
    replied
    The version of edgeR on the Bioconductor developmental repository has a function rpkm().

    Leave a comment:


  • Get the RPKM value of the genes analyzed using DESeq or edgeR

    Hi,

    I have done analyzation over RNA seq data using edgeR and DESeq to find DE genes (BAM files -> HTSeq -> edgeR and DEseq).
    For some comparisons I need to have the RPKM values related to each gene. What is the best way of getting it?

    Thank you in advance.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 11:09 AM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
144 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
118 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
111 views
0 likes
Last Post seqadmin  
Working...
X