MICRA: Frequently Asked Questions

How to use a personnal genome?

The user can give its own list of reference sequences. In this case, an NCBI ID file must be loaded.
If you want to use a personnal reference sequence which has not NCBI identifier, please contact us at MICRA_contact. We will add your reference sequence in a local directory not accessible to other users.

How to compare several samples?

If you have a project with several samples you want to compare, we advice you to follow this protocol:

  1. Run MICRA for one of the sample with your favorite parameters
  2. In the directory of the MICRA results, get the genomeList.txt file in the "reference_genomes" directory and if appropriated the plasmidList.txt file in the "reference_plasmids" directory.
  3. if you want to analyze both the genomes and plasmids, concatenate the two file in one file conataining all the reference sequences.
  4. Use this ID file as reference input in MICRA for the other samples
  5. Finally you can compare your samples with the MICRA comparison module.

How to reduce your input file size?

MICRA allows to upload a file up to 1 GB corresponding to a standard WGS microorganism sequencing run.
If your FASTQ file size is too big you can subsample your data. One way of doing this with Galaxy is as follows:

  1. Load your FASQ file in Galaxy.
  2. In NGS: QC and manipulation, use FASTQ Groomer to convert your FASTQ file.
  3. In Convert Formats, use FASTQ to Tabular converter to convert the FASTQ file produced in step 2 in tabular format producing one line for each four FASTQ lines.
  4. In Text Manipulation, use Select random lines from a file with the tabular file generated in step 3 and choose the number of lines you want to select in the field Randomly select.
  5. In Convert Formats, use the Tabular to FASTQ converter to convert the tabular file containing the n reads generated in step 4 into a FASTQ file containing a subsample of your original data (be careful to the column names).

What are the reads used in the analysis?

The MICRA pipeline do not include any pre-processing steps such as filtering or quality triming.
The reads given as input by the user are used directly in the analysis.
The user can clean his data himself before to run MICRA.

For how long my results are available?

Your results are available for 15 days before being deleted.

Are my data stored or used by MICRA or another person?

The files you load in MICRA website are deleted once your job is finished, so your data is not stored nor used by MICRA or another person.
Your results are available for 15 days before to be deleted and accessible only through the link providing by MICRA.
Your e-mail address is not diffused. It is used to send you your result link and could be used to send you important information about the MICRA pipeline (problems with MICRA or updates).

Technical troubleshooting

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