Question: How can I use Ion Reporter with 16S data for analysis of MG-RAST output?
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gravatar for tmad109
18 months ago by
tmad10910
tmad10910 wrote:

Hi, I am trying to convert a sequencing file which is in fna format to bcf or vcf. What tools do you think that will do this work? Many thanks, THilini

ADD COMMENTlink modified 18 months ago by Brian Bushnell15k • written 18 months ago by tmad10910

Where did you get this sequencing file? Normally sequencers output fastq, and I've never heard of one that generates reads with an fna extension - that usually indicates the file is a reference genome from a public database.

I think you need to explain the situation in much more detail to get a useful answer.

ADD REPLYlink modified 18 months ago • written 18 months ago by Brian Bushnell15k

Thank you, Brian. I imported the files from MG-RAST. They are gut microbial 16S sequences from Human Microbiome Project. I want to upload the files to Ion Reporter (IR) software to reanalyze. However, IR only accepts vcf and bcf files. That is why I want to convert fna files to vcf or bcf. Many thanks, Thilini

ADD REPLYlink written 18 months ago by tmad10910

.fna as in nucleotide fasta format, correct?

ADD REPLYlink written 18 months ago by genomax55k

Yes, you are right. Thank you.

ADD REPLYlink written 18 months ago by tmad10910

Was downloading the data as fastq format files an option? Ion reporter may be able to use those more effectively.

Are you sure about having/wanting to use Ion Reporter for what you are trying to do?

ADD REPLYlink written 18 months ago by genomax55k

I have not used Ion Reporter (or Ion Torrent) but it looks like it supports 16S metagenomics workflows. For those workflows, you would need either the raw or consensus reads, not vcf or bcf files; you need to double-check the documentation and make sure you are following a 16S workflow, not a variant-calling workflow. Your fna file might be consensus reads, or it might not (I've never used MG-RAST either). I feel like I don't know enough about the specifics of the topic to contribute usefully, so hopefully someone else with more experience will respond. I will adjust your title and tags.

ADD REPLYlink written 18 months ago by Brian Bushnell15k
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