How many reads used by a assembler for transcriptome assembly

Question

[seta]

Hi all,

I would like to know how many reads used by the assemblers, like Trinity and Soap-denovo trans tools for making a de novo transcriptome assembly? Mapping read back to the assembly is the right option? I usually run bowtie2 with default commands. Could you please put the important options to use the right command?

Thanks for sharing what you want.

Answer 1

[Antonio R. Franco]

I would say as many reads as possible. You can even mix the reads from different experiments

In the absence of a nice annotated reference genome, mapping to a transcriptome is perfectly valid