Quick Start¶
Importer¶
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
Operations¶
Validator¶
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¶
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
