Ion Torrent fastq files, Fastx_toolkit, and mothur

[fmoejes]

Hey everyone! Hope you're well!

Very new to this wonderful world of sequencing analysis!

Basically, as a result of Ion Torrent sequencing of 24 samples of 16S V6 rRNA I have fastq files (barcodes and primers have already been removed).

I carried out basic quality end trimming and passed them through a quality filter using the fastx_toolkit.

Now I want to map these 'cleaned' reads using mothur but I have NO idea where to start!

Help!!!!!

[GenoMax]

If you have access to the sff files then see this: http://www.mothur.org/wiki/Ion_Torre...s_using_Mothur

Other examples are on this page: http://www.mothur.org/wiki/Analysis_examples

[fmoejes]

Hey GenoMax! Thanks!

Would I need access to the sff files in order to carry out any further analyses with mothur?

[GenoMax]

Was waiting to see if someone will provide a more authoritative answer, but here goes. Since you have fastq files you could potentially pick a different pipeline that starts with those.

If you do have access to sff files then it would easy to follow the workflow linked above.

[fmoejes]

I see...

I'm definitely open to using a different pipeline!

Is there any you would recommend specifically for 16S V6 rRNA? The genomic DNA was extracted from samples that have a wide range of bacterial species, but not as wide as e.g. an environmental seawater sample.

[Sonica619]

GenoMax,you are so gentle.