Using reads from trimmomatic generated during a trinity run

[Jonathan Trieloff]

Hello

I'm a bit of a beginner, so sorry if this is obvious. I ran trinity with the trimmomatic flag. What does trinity actually use as the reads? It spits out some files in fastq format, two paired, two unpaired, and two PwU trimmed reads. Also, in the insilico_read_normalization directory, there are two PwU fastq files. What does trinity use as the read input? If I were to run trinity without trimmomatic, would I point to the normalized PwU fastq files to get the same result? Thanks!

[Brian Haas]

by default (when in silico normalization is enabled), Trinity uses just the 'P' paired fastqs from trimmomatic for assembly.  Those reads get fed into in silico normalization, and the normalized reads get assembled.