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Question: Does It Makes Sense To Assemble All My Rna-Seq Samples As Though They Were One?
2
gravatar for Ryan Thompson
8.0 years ago by
Ryan Thompson • 3.4k
TSRI, La Jolla, CA
Ryan Thompson • 3.4k wrote:

I am doing reference-guided transcript assembly and quantitifaction using Tophat and Cufflinks. Currently, I am running Cufflinks on each sample individually and then merging the assemblies with the cuffmerge tool. Would I get a better assembly by combining all the BAM files from all my samples into one and running Cufflinks on that? Or should it theoretically produce an identical assembly?

(Obviously the second strategy will yield nonsense FPKM values, but I can always requantify against each BAM file individually, so that's not a problem.)
assembly cufflinks transcript transcriptome • 2.3k views
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modified 4.9 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Ryan Thompson • 3.4k
1
gravatar for Bioinfosm
8.0 years ago by
Bioinfosm • 620
earth
Bioinfosm • 620 wrote:

I guess using all samples to make a topHat assembly would not make sense. I have seen a lot of groups combine the assembly from different samples, and then use that as the guide for tophat to get a better handle on transcripts (similar to what you are suggesting). Using data from all samples could actually confuse the assembly and yield inefficient transcript models to use with topHat!
ADD COMMENT • link written 8.0 years ago by Bioinfosm • 620

Even if the samples are from the same biological group ?

ADD REPLY • link written 7.1 years ago by Nicolas Rosewick ♦ 8.7k

Unless it is the same sample, you might be better off to run independent tophat analysis to find all the transcripts separately. Then there is always the option of combining all those to form the inclusive 'transcriptome'

ADD REPLY • link written 7.1 years ago by Bioinfosm • 620
0
gravatar for Nicolas Rosewick
7.1 years ago by
Nicolas Rosewick ♦ 8.7k
Belgium, Brussels
Nicolas Rosewick ♦ 8.7k wrote:

Hi,

Little additional question : Is it a good idea if the samples are from the same biological group ?

Thanks

N.
ADD COMMENT • link written 7.1 years ago by Nicolas Rosewick ♦ 8.7k
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