ISMARA sib logo small - Integrated System for Motif Activity Response Analysis

How to submit your data.

Data can be uploaded either through the ISMARA website , or by using the ISMARA uploader python script.

There are three possible ways to submit the data to ISMARA:

  1. Upload files from your own computer.
  2. Provide a list of URL links to the data files.
  3. Provide a list of SRR IDs.

Uploading files on the website

  • First provide your email address and a name for your project. ISMARA will notify you via email when its analysis of your data is ready, and use the project name for reference.
  • Select your data type, i.e. whether you have micro-array, RNA-seq, or ChIP-seq data.
  • Select the appropriate organism/genome assembly.
  • Inclusion of miRNA regulation in the analysis can be turned off if desired.
  • Click the "add files" button and select all the files you want to upload. Note you can click the button multiple times.
  • Click the "Start upload" button.
File formats
  • For micro-array data ISMARA expects CEL files. A list of supported Affymetrix chips is available here.
  • RNA-seq and ChIP-seq data can be provided as FASTQ, BED, BAM, or SAM files. Note that when using data that is already mapped it is essential that the genome assembly matches the one you selected above.
  • There should be one file per biological sample, except for paired-end FASTQ files. For paired-end FAST files, pairs of files with the name convention sampleX_R1.fastq and sampleX_R2.fastq should be used.
  • Choose informative files names because ISMARA will use the file names to refer to the samples in its results.
  • You are encouraged to compress your files with gzip or zip. Tar or zip archives with multiple files are allowed. Please do NOT use subdirectories in your archive.

List of URLS.

  • First make sure you provided a contact email and selected the correct data type and organism/genome assembly.
  • Paste URLs with the links to the data files (an example with two ftp URLs is provided).
  • There should be one line/URL per biological sample.
  • Click the "Submit links" button.

List of SRR IDs.

  • First make sure you provided a contact email and selected the correct data type and organism/genome assembly.
  • Paste the SRR IDs of the samples you wish to analyze (an example with two SRR IDs is provided).
  • You can annotate every SRR ID with a comprehensive name for better results representation. Just add add the name after the SRR ID separated by space.
     SRR1462350 Day0_rep1
     SRR1462356 Day3_rep1
  • Use one line per sample.
  • Click the "Submit SRR IDs" button.