Question: Pick De Novo OTUs Qiime
gravatar for Ruth M.
3.4 years ago by
Ruth M.10
Ruth M.10 wrote:

Hi Everyone,

I'm trying to on 50 samples (.fa files) that I have trimmed and aligned (not using QIIME). It seemed straightforward, but I can't get the input format of the data right. I thought it could be comma delineated, but it says that the file doesn't exist 'home/Data/KK.01.fa,KK.02.fa,KK.03B.fa,KK.04.fa,KK.05.fa' (command below) -i home/Data/KK.01.fa,KK.02.fa,KK.03B.fa,KK.04.fa,KK.05.fa -o home/Data/OTU&

I also tried using -i *.fa instead, but that gave the same result. When processing a large number of samples through the OTU picking, what is the proper way to input your files?

Thank you!!!

qiime otu • 1.3k views
ADD COMMENTlink modified 12 months ago by ankit hinsu10 • written 3.4 years ago by Ruth M.10

Thanks, I'm unable to run split_libraries_fastq, so I have alternatively trimmed my sequences and merged the paired reads so that I now have individual .fa files for each sample rather than the .fna file. I ended up writing out script for each one in a shell script and running it using bash, and it seems to be working.

ADD REPLYlink written 3.4 years ago by Ruth M.10
gravatar for Picasa
3.4 years ago by
Picasa480 wrote:

You need to run split_libraries_fastq before.

ADD COMMENTlink written 3.4 years ago by Picasa480
gravatar for ankit hinsu
12 months ago by
ankit hinsu10
ankit hinsu10 wrote:


I think that by this time, you might have received solution to your problem. Nevertheless, here is the solution.

  • QIIME1 requires input file in proper way (called QIIME-compatible format). Their tutorial "454 tutorial for de novo OTU picking" has a demultiplexing step. This step does three things: denmultiplexing, quality-filtering and combine all the sequences from all samples in QIIME-compatible way.

What you require is alternate to this step.

The answer is "" script. This script asks for a folder with all you input files and a mapping file having information about "which file belongs to which sample" [same mapping file used in QIIME with one extra column mentioning name of the file]. On running this script, it will combine all the sequences in QIIME-compatible format and produce a single fasta file (which you can use for OTU picking).

Hope it helps!!

ADD COMMENTlink written 12 months ago by ankit hinsu10
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