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Required files format

Louis-Mael Gueguen edited this page Oct 10, 2024 · 8 revisions

Kmdiff fof

The file must be tab-separated, with controls first:

control1: /path/to/control1_read1.fastq ; /path/to/control1_read2.fastq
control2: /path/to/control2_read1.fastq ; /path/to/control2_read2.fastq
control3: /path/to/control3_SE.fastq
case1: /path/to/case1_read1.fastq ; /path/to/case1_read2.fastq
case2: /path/to/case2_read1.fastq ; /path/to/case2_read2.fastq
case3: path/to/case3_SE.fastq

It can contain single-ends as well as paired-ends.

Snakemake config

In this config file, you can change several parameters:

  • the number of threads
  • minimum size of unitigs analysed to predict genes.
  • max memory used by Bcalm2 (in Mo)

You can also change the names of the conditions you experiment with for the run:

condition:
    - acne
    - healthy

Or change the paths, were the databases are and were the results will be. ❗ It is important that you give absolute paths and use double quotes " ❗.