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Output Files

In this page you can find an overview of the output files.

Expected output files

Upon successful execution of MIRFLOWZ, the tool automatically removes all intermediate files generated during the process.

The final outputs comprise:

  1. A SAM file containing alignments intersecting a pri-miR locus. These alignments intersect with (extended) start and positions specified in the provided pri-miR annotations. Please note that they may not contribute to the final counting and may not appear in the final table.

  2. A SAM file containing alignments intersecting a mature miRNA locus. Similar to the previous file, these alignments intersect with (extended) start and end positions specified in the provided miRNA annotations. Please note that they may not contribute to the final counting and may not appear in the final table.

  3. A BAM file containing the set of alignments contributing to the final counting and its corresponding index file (.bam.bai).

  4. Table(s) containing the counting data from all libraries for (iso)miRs and/or pri-miRs. Each row corresponds to a miRNA species, and each column represents a sample library. Each read is counted towards all the annotated miRNA species it aligns to, with 1/n, where n is the number of genomic and/or transcriptomic loci that read aligns to.

  5. OPTIONAL. ASCII-style pileups of read alignments produced for individual libraries, combinations of libraries and/or all libraries of a given run. The exact number and nature of the outputs depends on the workflow inputs/parameters. See the pileups section for a detailed description.

I want to keep the intermediate files

To retain all intermediate files, include --no-hooks in the workflow call.

snakemake \
--snakefile="path/to/Snakefile" \
--cores 4  \
--configfile="path/to/config.yaml" \
--software-deployment-method conda \
--printshellcmds \
--rerun-incomplete \
--no-hooks \
--verbose

After a successful execution of the workflow, the intermediate files are going to be found in the results/intermediates directory.

The following file structure is expected:

test/results/
├── pileups
│   ├── all
│   │   ├── check_file.txt
│   │   ├── all_samples.hsa-mir-A.min.1.pileup.tab
│   │   └── all_samples.hsa-mir-B.min.1.pileup.tab
│   ├── group_A
│   │   ├── check_file_group_A.txt
│   │   ├── group_A.hsa-mir-A.min.1.pileup.tab
│   │   └── group_A.hsa-mir-B.min.1.pileup.tab
│   └── lib_name
│       ├── check_file.txt
│       ├── lib_name.hsa-mir-A.min.1.pileup.tab
│       └── lib_name.hsa-mir-B.min.1.pileup.tab
├── TABLES
│   ├── all_mirna_counts.tab
│   └── all_pri-mir_counts.tab
└── lib_name
    ├── alignments_intersecting_mirna.sam
    ├── alignments_intersecting_mirna_uncollapsed_sorted.bam
    ├── alignments_intersecting_mirna_uncollapsed_sorted.bam.bai
    └── alignments_intersecting_primir.sam