This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Does It Makes Sense To Assemble All My Rna-Seq Samples As Though They Were One?

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.)

cufflinks transcriptome transcript assembly
• 4,029 views • link
updated by Biostar Biostar • written by Ryan Thompson Ryan Thompson

2 answers

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!

• 2 views • link
written by Bioinfosm Bioinfosm

Even if the samples are from the same biological group ?

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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'

• 0 views • link
written by Bioinfosm Bioinfosm

Hi,

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

Thanks

N.

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

Log in to answer this question.

More posts like this