Output¶
GFF command¶
The mirtop gff
generates the GFF3 adapter format to capture miRNA variations. The output is explained here.
Stats command¶
The mirtop stats
generates a table with different statistics for each type of isomiRs:
- total counts
- average counts
- total sequences
It generates as well a JSON file with the same information to be integrated easily with QC tools like MultiQC.
Compare command¶
The mirtop compare
generates a tabular file with information about the difference and similarities. The first file in the command line will be considered the reference and the following files will be compared to the reference. Each line of the output has the following information for each file:
- sample
- idu
- seq
- tag:
E
if not in reference,D
detected in both,M
missing in target file - same_mirna: if the sequence map to the same miRNA in the reference and target file
- one column for each isomiR type with the following tags:
FP
(variation not in reference),TP
(variation in both),FN
(variation not in target file)
Counts command¶
The mirtop counts
generates a tabular file with the following columns:
- unique identifier
- read sequence
- miRNA name
- Variant attribute from GFF3 column
- One column for each isomiR type showing the exact variation
- One column for each sample with the counts for that sequence
Export command¶
The mirtop export
generates different files from a mirGFF3 file:
- isomiRs compatible files
- FASTA files
- VCF files