Merging transcriptomes coming from SRA: caveats and best practices?

[Clammomatic]

I'm about to start a project where I want to pool all existing transcriptomes in SRA for a nonmodel species without reference genome to study differentially expressed genes and the kind. Might worth mentioning that the transcriptomes I want to pool mostly come from different tissues.

Have you ever done something similar? Is there anything I should be extra careful about (batch effect, ...)? Do you have some literature suggestion about something similar to my project? I only found papers about merging microarray data until now.

[colindaven]

Hmm. You might want to use the aggregated webstores of RNA-seq like recount2 or others.

https://jhubiostatistics.shinyapps.io/recount/

I would combine and put them into a nice web tool like the DEGUST webserver to do some MDS and check quality. Or use R and PCA locally.