Paired-end and single-end reads combined during RNAseq - acceptable?

Question

[iktu23]

Good day,

For my RNAseq experiment (plant) I needed to construct a de novo assembly (no genome). Due to financial constraints we could only sequence one of the three biological replicates as paired-end. The other two were single-end. Everything else was processes in the same way.

My question is - can you combined the PE and SE reads together, or must I only use the forward reads from all?

I have not found a paper that uses both.

Thank you in advance!

Answer 1

[FGV]

For a de-novo assembly PE reads are actually the most informative and it is usually advisable to have several PE libraries with different insert sizes (e.g. here)

You can combine together PE and SE reads and there are several programs that allow for it (e.g. Velvet). You can also get some more info here

[iktu23]

Thank you! I have constructed my assembly using Trinity, and run my DEG analysis using edgeR. Things look good, but I just had a realisation that I haven't seen any references specifying that they combined PE with SE. I'm relieved you said one can combine them, so thank you!

Answer 2

[Dattatray Mongad]

There is not a problem at all as long as the assembly of both the reads are significantly similar.