Question: Newbie wanting to align Ion Torrent PGM data to mitochondrial DNA template
0
gravatar for mpugh
5 months ago by
mpugh0
mpugh0 wrote:

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 mepugh@vims.edu

alignment • 192 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson23k • written 5 months ago by mpugh0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson23k
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