Hello, I just posted a comment about trimming in another thread. Now I would like to ask anyone who has experience (or any desire to share their two cents) to offer some feedback that might help me and other "newbies" dealing with NGS data and the different tools out there. I am relatively new to this and am now dealing with A LOT of data from 3 different projects all at once. I am finding that some tools are just not worth it - but maybe that is just ignorance on my part. I'm copying my comment here and I'm asking what do you think?
ORIGINAL comment added to thread "Trimmomatic: Trimming only custom adapter sequences":
Hello to anyone new to bioinformatics who is reading this to try and solve a problem trimming with trimmomatic. I wish I had read this post a week ago and saved myself many headaches. Please save yourself time and go use trim-galore (which uses cutadapt as part of the process) or just cutadapt (or another alternative like bbtrim, which is supposed to work well too). I did finally get trimmomatic to work (many hours and finally help from an IT person). It was a big waste because it runs VERY slowly (even on a high powered compute system) and it did not give consistent output. A lot of the adapters were not removed when I got the reads and ran them on fastqc afterwards.
I then ran everything using trim-galore (installed with miniconda 3 from the bioconda channel) and got VERY fast and very clean reads that were also trimmed properly for quality and already run through fastqc (you can choose that option easily). I also found out it is easy to add an additional unique adapter sequence to trim out at the same time, and I ran trim-galore on a different dataset (produced by a flavor of radseq) and was able to get rid of the regular illumina adapters and the unique adapter.