RNA-seq analysis without replicates using tximport and DESeq2
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@endre-sebestyen-2707
Last seen 16 months ago
Hungary, Budapest

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 • 951 views
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I am interested in this thread.

Would you mind to share your code once done ?

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@mikelove
Last seen 3 hours ago
United States

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.

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