Which of the output files of TrimGalore! must I align?

Question

[vinayjrao]

Hello,

I have been working on some whole exome sequencing data, and although I get the jist of the pipeline, in some of the samples I'm currently handling, I found adapter sequences, which were trimmed using TrimGalore! However, TrimGalore! generates to output files - filename_trimmed.fq.gz and filename_val.fq.gz. When I looked into the report, it mentions these two lines

Writing final adapter and quality trimmed output to filename_trimmed.fq.gz

and

Writing validated reads to filename_val.fq.gz

I am now confused on which file to push into alignment and the downstream steps. I think it is filename_val.fq.gz due to the description of the two files, but if I have to align filename_trimmed.fq.gz, kindly explain why.

Thanks in advance.

[GenoMax]

Can you post your trimgalore command?