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Frequently Asked Questions

  1. Do I have to upload my RNA-seq data?
  2. Is the RNA-seq data that I uploaded kept confidential?
  3. What types of raw RNA-seq data does EcoOmicsAnalyst accept?
  4. Do I need to register to use EcoOmicsAnalyst?
  5. How can I upload my raw RNA-seq data files?
  6. How many samples can I upload for an analysis?
  7. FileZilla gave the error "Response 550: Forbidden filename". What does it mean?
  8. How long will it take to upload my files?
  1. Do I have to upload my RNA-seq data?

    If you want to use EOA online (this site) and your data is less than 30GB, you have to upload your data to our server. The bottleneck is the slow data uploading.
    Therefore, you are encouraged to use the EOA local version here, which can be easily installed in your local computer with a docker image. This will save your tremendous time for data uploading.

  2. Is the RNA-seq data that I uploaded kept confidential?

    Yes. The data files you upload for analysis as well as any analysis results, are not downloaded or examined in any way by the administrators, unless required for system maintenance and troubleshooting.
    All raw data files will be deleted automatically after 30 days, while the result files will be kept until you delete your project or user account; and no archives or backups are kept. You are advised to perform the analysis immediately after uploading all your samples.

  3. What types of raw RNA-seq data does EcoOmicsAnalyst accept?

    EcoOmicsAnalyst accepts raw RNA-seq data and does not require pre-processing such as quality control, error correction, ploy(A) tail removing.
    The raw RNA-seq data can be paired- or single- end reads and must be compressed with file extension of .fastq.gz/.fq.gz.

    For organisms with transcriptome references:
    EcoOmicsAnalyst employs Fastp (click here) for raw reads quality check, before submitting to Kallisto (click here) for ultra-fast pseudoalignment gene quantification.

    For organisms without transcriptome references:
    EcoOmicsAnalyst employs Seq2Fun (click here) (Peng Liu, et al. (2021) “Ultrafast functional profiling of RNA-seq data for nonmodel organisms” Genome Research), which is a novel and high-performance RNA-seq data quantification tool for non-model organisms without genome references, to do ortholog quantification. (see details in Data Processing and/or (click here)).

  4. Do I need to register to use EcoOmicsAnalyst?

    To use the EcoOmicsAnalyst RNA-seq module, you are required to register via a valid email address (click here).
    Trying our example data is registration-free.

  5. How can I upload my raw RNA-seq data files?

    Due to the large size of RNA-seq data, you are only allowed to upload your raw RNA-seq data via FTP Clients tools such as FileZilla.

    1. Please click here to download FileZilla and install it locally.
    2. Then connect with our server using Host: dev.ecoomicsanalyst.ca and your registered email and password with port 21.
    3. Click File -> Site Manager -> New site -> Fill the fields of Host, Port, User and Password.
    4. Click Transfer Settings -> select Active -> click Connect.
    5. Drag all your files in local to our server.
    6. Please monitor your file uploading in the FileZilla. Once all your files are successfully uploaded and please login again to process.
    7. Once your job is submitted, please do not remove or upload any files in FileZilla.
    Please check more details in our TUTORIALS (click here).
    Note: your storage quota is 30GB, and your raw data will be kept for 30 days. If you have a data set more than 30GB, please split them, upload and run, then delete files in storage from FileZilla before you can submit new dataset.

  6. How many samples can I upload for an analysis?

    There is no limitation of number of samples allowed to be upload, but the storage for your samples is limited to 30 GB. To process datasets larger than 30GB, we recommend splitting the samples into multiple groups, deleting each set of files from your account after they have been processed.

  7. FileZilla gave the error "Response 550: Forbidden filename". What does it mean?

    This usually means that you tried to upload a file that is not in compressed FASTQ format. This will be the case if the filenames do not end in ".fastq.gz". Uncompressed FASTQ files are extremely large and will take too long to upload to the EOA server.

  8. How long will it take to upload my files?

    Data upload is typically the most challenging step of using EOA, since FASTQ files are extremely large and must be uploaded over a network connection. The upload time will depend on both your file size and your network speed. In our own tests on a laptop and home wifi network, it took ~30 minutes to upload one FASTQ file that was ~2.5GB. So, a full dataset could take between 5-10 hours to upload.

    Maintaining a constant network connection for this long could be challenging and could take up internet bandwidth, so we suggest starting file upload in the evening. Internet speed is usually fastest at night, and files will be ready to process in the morning.

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