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miRNA-FeatureCounts

This is a python snakemake file which creates feature counts table for miRNA sequences combining cutadapt function and bowtie2 reference alignment.

Currently Loaded Modules:

  1. python/py37-anaconda-2019.10 2) snakemake/5.7.1-py37 3) gbc-cutadapt/2.10 4) gbc-bowtie2/2.4.1 5) subread/2.0.1

Step-by-step analysis:

  1. Activate the python anaconda-snakemake environment. conda activate snakemake

  2. Edit the config.json file according to your data and file paths.

  3. Ensure that meta-table contains all the necessary fields.

** NOTE EXACT HEADERS HAVE TO BE ENFORCED WITH ONLY ONE SPACE BETWEEN THE ENTERIES or key errors will be thrown during processing**

  1. Try the dry run of the snakefile created to check any potential errors. snakemake -n -s Snakefile

  2. Launch all the jobs.

Launching the jobs:

snakemake --latency-wait 120 -p -j 100 -s Snakefile

  1. The pipeline will produce a countfinal.txt file containing all the details of the miRNA sequences required along with an output directory with all the trimmed and mapped reads.