I used Trinity to assemble ~700M paired-end reads using the following command

"Trinity.pl --seqType fq --left left.fq --right right.fq --SS_lib_type FR --output ./ --JM 300G --CPU 15"

The run was successful, and I got a list of contigs.

Now I realize that the data was not strand specific, and I am wondering how does the adding of "--SS_lib_type FR" parameter affect the assembly.

Shall I redo the assembly?

Thanks

Mali