Frequently Asked Questions

  1. How to submit a request to the RNAMiner web service?
    • First, prepare RNA-Seq reads files (.fastq). The acceptable formats of the RNAMiner web service include ".fastq.gz" and ".fastq.tar.gz".
    • Second, choose the analysis categories. RNAMiner includes five analysis categories: mapping RNA-Seq reads to reference genomes, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. Each category needs the results in the previous categories. If you choose one category, the previous categories will be executed automatically. For example, if you choose "predicting gene functions", the first three categories will be executed automatically.
    • Third, choose the species. RNAMiner can analyze data on four species: Human, Mouse, Drosophila Melanogaster, and TAIR10 Arabidopsis at present.
    • Fourth, choose criterion of identifying differentially expressed genes. It is p-value or q-value.
    • Fifth, set the threshold of p-value or q-value. The value should be between 0 and 1, and the default value is 0.05.
    • Sixth, input email address. A link to the data analysis results will be sent to this email address.
    • Seventh, input sample names. The last three categories request users to upload files for 2 samples.
    • Eighth, upload reads files. Users can upload more than one reads files for each sample.
    • Last, click "Submit".
  2. How can I receive the data analysis results?
    • When the data analysis is finished, you will receive an email with a link. You can click the link to view and download the data analysis results.
  3. When will I receive the data analysis results?
    • The time expense of analyzing a set of RNA-Seq data depends on how big the data is, how many reads files there are in the data set, and how many jobs there are in the waiting queue. Normally a data analysis can be finished in several hours. However, you have to wait if there are too many jobs in the waiting queue which were submitted before your request. Our server cannot handle too many jobs at the same time because of CPU and space limitations.
  4. May I submit multiple requests to the RNAMiner web service?
    • If you submitted one request to the RNAMiner web service and it is running or it is in the waiting queue, you cannot submit another request. You have to wait till your previous job is finished.
  5. Is there any test data in the RNAMiner web service?
    • The RNAMiner web service provides users with a test data in the home page with two samples and two replicates in each sample. The species is Human.
  6. How can I contact you if I encounter any problems about the RNAMiner web service?
    • If you have any problems, questions, or suggestions about the RNAMiner web service, please email to RNAMiner@gmail.com. We will reply to you as soon as possible.

   

Bioinformatics, Data Mining and Machine Learning Laboratory, Department of Computer Science, University of Missouri