Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • sdriscoll
    replied
    I'm not sure if you need anything much more exotic than a mean of the two separate expressions.

    *edit* scratch that. a mean isn't quite right. calculating expressions is pretty easy when you have the raw components and when you have those you can easily combine expressions but when you only have two separate expressions then i'm not sure how to do it.

    for example, say we have some gene X of length 3400 bases.

    sample A has 12000 reads of aligned to the gene, 34,123,123 reads aligned
    sample B has 5161 reads aligned to the gene, 25,321,321 reads aligned total

    sample A RPKM = (reads*1e9)/(reads_aligned * length) = (12000*1e9)/(34,123,123*3400) = 103.43
    sample B RPKM = (5161*1e9)/(25,321,321 * 3400) = 59.95

    mean of those expressions = (103.43+59.95)/2 = 81.69

    RPKM of merged samples = ((12000+5161)*1e9)/((34,123,123+25,321,321)*3400) = 84.91

    the weighted mean works but you need to know the # of millions of mapped reads to use as the weights:

    weighted mean of samples = (103.43*34,123,123 + 59.95*25,321,321)/(34,123,123+25,321,321) = 84.91

    i don't think cufflinks reports what the normalization factor is it uses for FPKM calculation so i'm not sure you'll find an easy way to merge them. I guess you have no choice but to run them combined as a single BAM.
    Last edited by sdriscoll; 04-30-2012, 04:35 PM.

    Leave a comment:


  • vinay052003
    replied
    Yes.. Is there any good way?

    Leave a comment:


  • sdriscoll
    replied
    Cufflinks needs to know your insert size and standard deviation. In fact it will figure it out from your alignments. Since that information is apparently necessary for it to do it's work then you should probably keep those alignments separate through cufflinks. I get you, though, you want one set of expressions not two. Right?

    Leave a comment:


  • vinay052003
    replied
    That's a good idea. I thought of that as well. Actually in the end I also need the expression of each transcript. And after merging assemblies, in order to estimate the expression, I'll need to use two bam files anyways. That's why I was wondering weather to mege bam files before running the Cufflinks or to do it later.
    Any thoughts?
    Thanks.

    Leave a comment:


  • sdriscoll
    replied
    I don't think it will matter in the end. If you are going to use Cufflinks then with two separate alignments you'll have to use cuffmerge to merge the separate transcript annotations into a single consensus annotation. At that point the information from both runs of the sample will be merged. In fact everything will probably go smoother if you just run them through cufflinks separately and follow that with cuffmerge.

    Leave a comment:


  • Merge from multiple libraries + tophat + cufflinks

    Hi,
    I have two paired-end sequencing RNA-Seq libraries. Both of them are from the same sample but prepared using different insert lengths. I've run tophat on both of them separately. Now I want to run Cufflinks. I was wondering if it is a good idea to merge tophat accepted_hits.bam files for different insert lengths and run Cuffllinks on the merge file?
    My goal is to detect splice variants for the whole sample.

    Thanks

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-23-2024, 04:11 PM
1 response
22 views
0 likes
Last Post kim897
by kim897
 
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
58 views
0 likes
Last Post seqadmin  
Working...
X