I need to merge several QIIME runs done from Illumina sequencing. There are instructions on how to merge the biom files and mapping files (I've already done the mapping file) but nothing exists on how to merge rep_set.fna files. Can one just concatenate them? Wouldn't that result in some duplicate rep_sets? And if so, would that affect me downstream (when I have to make my phylogenetic tree for unifrac)?
Based on the information you have provided, I can give some suggestions. Regarding first part of question, If you can combine mapping files, then you can also combined rep_sets. Each rep_set sequence gets id from OTU number and sample ID. You can just concatenate as you said.
But for the second part of question, you might have duplicate rep_set with different seq ID, although they are same OTUs. I had similar problem. If you have different sample ID, you can actually combine the sequence files after quality control and pick OTUs (clustering) on the combined sequence file (big single file). This will solve the duplicate sequence in rep_set and you will have single OTU table (big one will all the samples).
There might be other solutions, I will eager to read other suggestions.
If I am dealing with multiple sequencing files I usually merge the denoised files by concatenating them. Then I go on to the pick_otus.py step using the concatenated file as input. This should generate a uclust folder which you can then use in the pick_rep_set.py step to generate the rep_set.fna file.
Our workflow for multiple sequence runs is to cat all the files after split library so we don't duplicate OTUs.
Workflow:
split_library.py on each separate run
Put all the seqs.fna from the split_library commands in a single folder
run cat *.fna > combined_seqs.fna
combine all the mapping files in LibreOffice and save as a tab seperated .csv
Then proceed with your pipeline
We do de novo OTU picking so all of our sequences have to be combined before OTU picking.
I am really new in Qiime and bioinformatics stuff, I would like to know what is the meaning of this command :
Write non-singleton otus representative sequences from step1 to the final rep set file or
Write non-singleton otus representative sequences from step 2 and step 4 to the final representative set and the new reference set (151227_otus_2//rep_set.fna and 151227_otus_2//new_refseqs.fna respectively)
it means I should only copy and put in the 151227_otus_2 folder?
Hi All,
How do you handle the same barcode being used for different sites/samples when concat the mapping files?
When using QIIME, don't you have the option of picking otus for a list of seq.fna files? For example:
pick_open_reference_otus.py -i $PWD/seqs1.fna,$PWD/seqs2.fna -r $PWD/refseqs.fna -o $PWD/ucrss_iter/ -s 0.1 -p $PWD/ucrss_params.txt
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