I have two SE librarys I need to assemble together with Trinity.
Library one has 7928922 read pairs
Library two has 7884975 read pairs
What is the correct way to do this?
not sure what you mean by SE libraries, but if these are both read pairs, then you can just concatenate the files, left with left, right with right.
The paired information is in the read header (should end in /1 or /2) so it shouldn't matter if they are different libraries.
Background:
I was given two libraries (A+B) which were PE non-strand-specific. Each library had read pairs (A_1.fq, A_2.fq, B_1.fq, B_2.fq).
I used FLASH to merge the mate-pairs. So, A_1.fq + A_2.fq = A3.fq and B_1.fq + B_2.fq =B3.fq.
It is my understanding that once you merge mate pairs you end up with a single-end library. If this is the case, is it acceptable to simply merge the SE files together and run in Trinity?
cat A3.fq B3.fq > merged.fq
Trinity --seqType fq --JM 750G --single merged.fq --SS_lib_type F --CPU 24
