Hello,
I have followed the miseq SOP. And everything went well. However i have some confusions regarding two things
1) Input data: Currently I have used Mothur test data from Miseq.
Input data can be : Illumina or 454
(1.1) Illumina
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single end + fasta files => Can we create stability file for that. If yes how is the quality handled? and what steps top follow next.
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single end + de-multiplexed fastq files => for this i guess trim.seq command with oligos file is required. Then it will create de-multiplex fastq file? and what next ?
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paired end + de-multiplexed fastq files => for this i guess trim.seq command with oligos file is required
Then it will create de-multiplex fastq file? and can I then use these files to create stability file and follow up Miseq SOP steps
(1.2) 454
It is more or less clear from SOP or To be honest I have not tested it yet
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2) Biom file: To create Biom file in mothur one can provide metadata file, shared file, constaxonomy file, reftaxonomy(for picrust).
What is not clear to me is
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How is mothur handling the sub-sampled shared file with not sub-sampled taxonomy file.
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When i would like to use phyloseq package for visualizations, with individual files then the constaxonomy and sub-sampled shared file don’t contain same ids. How can that be handled
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Finally, how can I add phylogenetic tree file to biom file? When try to merge it with Phyloseq the content doesn’t match.
Looking forward for some clarity
Thank you