How do I combine reads?

How do I combine paired-end and single-end reads?

Our recommendation for doing this has changed over time and across different Trinity software versions. Trinity doesn't have great support for using mixed single-end and paired-end data, and the setup process for shoe-horning the data into Trinity involves a few manual steps.

1. If you want to quality trim your data, run Trimmomatic (or other) directly.

2. Run in silico normalization separately for each of your libraries.

3. Combine all your reads into one fastq file. If your data are strand-specific, orient your reads to all the sense transcript orientation.

4. Run Trinity like so:

   % Trinity --single combined_reads.fastq --no_normalize_reads --run_as_paired ...

if your data are strand-specific and were oriented to the forward strand orientation, be sure to include '--SS_lib_type F'

How do I combine strand-specific and non-strand-specific reads?

There is no good way to combine strand-specific data with non-strand-specific data, unless you decide to treat the entire data set as non-strand-specific.