Trinity denovo transcript multiple reps paired ends

[nimrod337]

Sorry if this is in the wrong place. There are quite a few spots this could have gone. I've done some poking around, and haven't quite found an answer to my question, which is:

I am attempting to assemble a denovo transcript using paired end illumina 3000 reads from 4 different treatments, with 3 biological reps per treatment.

To do an assembly de novo, is it kosher (or better yet, is it required) to join all the reps from all the treatments into one "super-reads" file for R1 and another for the R2? If so, do I have to cat them in the same order to allow the correct R1 read to pair with its correct R2 read? Is there anyway to avoid this, and just give trinity all of the read files individually?

[nimrod337]

I figured it out. I can add multiple files, so long as they are separated by a comma, not a space. So my new question is: can I load paired end reads using --left, --right, and also include my singleton reads in the same run?

How would that effect my --SS_lib_type <string> argument?

[westerman]

I haven't done this but the answer as per the authors (via the Trinity mailing list a year or so ago) is to add the singleton reads to the end of the left reads.

[nimrod337]

So I can just add the singleton files to the end of my --left file1.fastq,file2.fastq,etc.....,singleton1.fastq,singleton2.fastq ? This will result in 12 fastq files after --right, and 24 files after --left. I'll give it a shot, and see what happens.

Thanks for the reply!