I have three large .fastaq files for an Ion Torrent PGM analysis for three species of tuna. I want to align them against a mtDNA template for tuna. I have looked at the Galaxy tutorial but it does not address what I want to. I have done the FastQC runs and for the most part they look good. My understanding is that I am to trim the segments- I am presuming that means the adapters and barcodes, and/or the larger pieces (>200 bases), or something else? I would appreciate any advice, a link to a tutorial, or whatever one feels necessary for me to accomplish my goal. I thank all in advance. Sincerely, Michael Eugene Pugh visiting scientist VA Institute of Marine Science email@example.com
Help for using Ion Torrent data in Galaxy is in this prior Q&A: https://biostar.usegalaxy.org/p/22071/
If you need more details about protocol best-practises and options, reviewing current publications or asking/reviewing prior questions at a general bioinformatics forum such as https://www.biostars.org/ would be a good choice.
Thanks! Jen, Galaxy team