Bioportal and CLOTU Tutorial

CLOTU is an online pipeline for processing and clustering of 454 amplicon reads into OTUs (Operational Taxonomic unit) followed by taxonomic annotation. CLOTU is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal webbased bioinformatics service (http://www.bioportal.uio.no).

Bioportal Registration

Using Bioportal

Useful links
Bioportal tutorial https://wiki.uio.no/usit/suf/vd/hpc/index.php/OSCG:Tutorial List of applications on Bioportal http://www.bioportal.uio.no/appinfo/ Computing infrastructure behind Bioportal https://wiki.uio.no/usit/suf/vd/hpc/index.php/TITAN CLOTU (brief description page) on Bioportal http://www.bioportal.uio.no/appinfo/show.php?app=CLOTU CLOTU Example dataset http://www.bioportal.uio.no/onlinemat/online_material.php Download the following 3 files on local disk: 1. Sequence data file (.zip) 2. TPA_file.txt 3. METADATA.txt

Uploading data file and submitting CLOTU job on Bioportal Upon successful Login: 1. If this is the first time you have logged on, you can upload your data files in my_project, or can create new project using PROJECT button (e.g. clotu_data). 2. Upload data files for CLOTU analysis in project created in previous step (e.g. clotu_data or my_project) using FILE-ADMIN section. 3. To submit a CLOTU job or start analysis, use SUBMIT JOB button. The next page contains boxes namely Project, Input files, Application, and Submit job. Project and Input files box are linked, choose your project using pull down menu, the corresponding files uploaded in that particular project will appear in Input file box. a. Select your input files. b. In Application box, select the application CLOTU@titan from the pull down menu option. c. Type in a job name e.g. Clotu_run_1 Once you click on submit button, the user is then provided with all the parameters you can set for CLOTU analysis. The same procedure as explained in step 3 can be followed for any application you want to run on Bioportal (You must be aware of the input files required for such applications). 4. Select Filtering/Trimming, Clustering, and BLAST parameters for CLOTU analysis. 5. Since the dataset we are analysing is not very large, so we can leave

the Queue Options to their default values. 6. In Account information box select bpcourse to skip the queue for now. If bpcourse option is not available select bioportal. (bpcourse queue will be removed after this week, use bioportal if you want to analyse your own dataset). Go to bioportal tutorial for more information about all queues available on Bioportal (https://wiki.uio.no/usit/suf/vd/hpc/index.php/OSCG:Tutorial#Submitti ng_Jobs) 7. Clicking Start Computation submits the job. To start another job with different parameters repeat step 3 to step 7. Exercise: Submit 2 CLOTU jobs on Bioportal using example dataset, each with different clustering method (blastclust and cdhit) and compare the OTUs resulted from either clustering methods?

Status of Jobs submitted Use JOB ADMIN button to check the status of the job submitted. Go to Managing your jobs section of Bioportal tutorial for more information about each of the status (https://wiki.uio.no/usit/suf/vd/hpc/index.php/OSCG:Tutorial#Managing_ Your_Jobs). Viewing a Job and Downloading result files Once the status of job submitted shows Completed/Finished. You can select that job and use view button to results files of CLOTU or use download button for viewing result files on local disk. Brief descriptions of all the result files downloaded are at CLOTU description page on Bioportal

(https://www.bioportal.uio.no/appinfo/show.php?app=CLOTU).