Question: RNA-seq analysis without replicates using tximport and DESeq2
1
gravatar for Endre Sebestyen
2.9 years ago by
Endre Sebestyen60 wrote:

Hi all,

I need to reanalyse an RNA-seq experiment with 2 conditions and unfortunately no replicates. I probably don't have big changes in expression, 100-200 genes with logFC max 2-3.

I'm planning to do the the following:

  1. Salmon/Kallisto with a recent RefSeq collection to estimate read counts.
  2. tximport to import gene level counts with an offset that corrects for changes to the average transcript length across samples.
  3. DESeq2 with all the warnings read in the manual.
  4. Rank genes based on lfc, and compare it to other stuff

Any thoughts on this? Can I improve it in any way?

rnaseq deseq2 tximport • 663 views
ADD COMMENTlink modified 2.9 years ago by Michael Love25k • written 2.9 years ago by Endre Sebestyen60

I am interested in this thread.

Would you mind to share your code once done ?

ADD REPLYlink written 2.9 years ago by arfranco130
Answer: RNA-seq analysis without replicates using tximport and DESeq2
1
gravatar for Michael Love
2.9 years ago by
Michael Love25k
United States
Michael Love25k wrote:

hi Endre,

I like the pipeline you've set up here. MA plot will be most revealing. The p-values are not of any use, but the moderated LFCs can help with ranking genes for follow-up.

ADD COMMENTlink written 2.9 years ago by Michael Love25k
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