Quick Start


From Bam files to GFF3

git clone mirtop
cd mirtop/data

You can use the example data. Here the reads have been mapped to the precursor sequences.

mirtop gff -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam

From seqbuster::miraligner files to GFF3

miRNA annotation generated from miraligner tool:

mirtop gff --format seqbuster --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out examples/seqbuster/reads.mirna

From sRNAbench files to GFF3

miRNA annotation generated from sRNAbench tool:

mirtop gff --format sranbench -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out srnabench examples/srnabench

From PROST! files to GFF3

miRNA annotation generated from PROST! tool. Export isomiRs tab from excel file to a tabular text format file.

mirtop gff --format prost -sps hsa --hairpin  examples/annotate/hairpin.fa --gtf  examples/annotate/hsa.gff3 -o test_out examples/prost/prost.example.txt

From isomiR-SEA files to GFF3

miRNA annotation generated from isomiR-SEA tool.

mirtop validate examples/gff/correct_file.gff



To validate your mirGFF3 file and make sure if follows the current format:

mirtop gff --format isomirsea -sps hsa --hairpin  examples/annotate/hairpin.fa --gtf  examples/annotate/hsa.gff3 -o  test_out examples/isomir-sea/tagMir-all.gff

Get statistics from GFF

Get number of isomiRs and miRNAs annotated in the GFF file by isomiR category.

cd mirtop/data
mirtop stats -o test_out example/gff/correct_file.gff

Compare GFF file with reference

Compare the sequences from two or more GFF files. The first one will be used as the reference data.

cd mirtop/data
mirtop compare -o test_out example/gff/correct_file.gff example/gff/alternative.gff

Updates mirGFF3

Updates older versions with the most current one.

cd mirtop/data
mirtop update -o test_out_mirs examples/versions/version1.0.gff


Export file to isomiRs format

To be compatible with isomiRs bioconductor package use:

cd mirtop/data
mirtop export -o test_out_mirs --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/gff correct_file.gff                                   

Export file to FASTA format

cd mirtop/data
mirtop export -o test_out_mirs --format fasta -d -vd --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/gff/correct_file.gff

Export file to VCF format

cd mirtop/data
mirtop export -o test_out_mirs --format vcf --hairpin examples/annotate/hairpin.fa --gtf examples/a
nnotate/hsa.gff3 examples/gff/correct_file.gff

Get count file

This file it is useful to load into R as a matrix. It contains the minimal information about each sequence and the count data in columns for each samples.

cd mirtop/data
mirtop counts -o test_out_mirs --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/synthetic/let7a-5p.gtf