Question: How do I combine multiple SE libraries in a single Trinity run?
gravatar for moldach
3.6 years ago by
moldach0 wrote:

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?

trinity galaxy rna-seq pe • 1.5k views
ADD COMMENTlink modified 3.6 years ago by wrf0 • written 3.6 years ago by moldach0
gravatar for wrf
3.6 years ago by
wrf0 wrote:

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.

ADD COMMENTlink written 3.6 years ago by wrf0


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

ADD REPLYlink written 3.6 years ago by moldach0
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