De novo RNA-Seq Assembly using Trinity with variable length reads

[illuminaGA]

Dear All, i am working on a project that will do De novo RNA-Seq Assembly using Trinity. Totally have 16 samples from 2 projects.

1. 8 sample, PE150, 30x, Hiseq 2500
2. another 8 sample, PE300, 100x, Miseq

I am wondering that if the Trinity can take the reads with variable length reads? and is there any technical and biological differences impact on the result if the data from a different condition, platform, and reads lengths?

Can you please give me some pointers? Appreciate it.

[gringer]

That should be fine. Inchworm does a kmer-based assembly, so as long as the reads are longer than the size of the kmers, it should be okay.

However, it'd be a good idea to do adapter and end trimming on the reads, particularly for the longer 300bp sequences.

You'll get a more informative transcriptome from combining reads that are from multiple samples, because it increases the chance that any transcript will have sufficient coverage for good assemblies.