Galaxy |

NanopolishComp: FreqMethCalculate (version 0.6.11+galaxy1)

Select nanopolish call methylation file:

Set minimal number of reads covering a site to be reported:

Select fasta index file:

Obtained with samtools faidx. Required for coordinate sorting

Set sample ID:

Used for bed track header.

Are sites strand specific?:

Set minimal log likelyhood ratio:

To consider a site significantly methylated or unmethylated.

Select output file(s):

What it does

NanopolishComp is a companion package for downstream analyses of Nanopolish output files.

Freq_meth_calculate calculates methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.

Input

A nanopolish call methylation tabular output file.

Output

BED file

Standard genomic BED6. The score correspond to the methylation frequency multiplied by 1000. The file is sorted by coordinates and can be rendered with a genome browser such as IGV

Tabulated TSV file

Contrary to the bed file, in the tabulated report, positions are ordered by decreasing methylation frequency.

The file contains the following fields:

chrom / start / end / strand: Genomic coordinates of the motif or group of motifs in case split_group was not selected.
site_id: Unique integer identifier of the genomic position.
methylated_reads / unmethylated_reads / ambiguous_reads: Number of reads at a given genomic location with a higher likelyhood of being methylated or unmethylated or with an ambiguous methylation call.
sequence: -5 to +5 sequence of the motif or group of motifs in case split_group was not selected.
num_motifs: Number of motif in the group.
meth_freq: Methylation frequency (out of non anbiguous calls).

References

More information are available on the project website and github.