Compare methylation levels at transcriptome sites, summarized by gene, with dmr compare-tx-sites
The dmr compare-tx-sites allows you to compare modifications between two conditions.
This command uses a transcriptome-aligned bedMethyl table and maps the coordinates from each transcript to common gene coordinates.
After which, the modification counts from each isoform are combined making a gene-level pileup.
The gene-level modifications are then compared using the same method as dmr isoform.
Example command:
This command uses two bedMethyl tables corresponding to two conditions to be compared. These bedMethyl tables are expected to be bgzipped and have tabix indices.
modkit dmr compare-tx-sites \
-a ${bedmethyl_a} \
-b ${bedmethyl_b} \
--out ${output.bed} \
--gtf ${gtf}
A volcano plot can be also made, using the following extra options. An example is below.
modkit dmr compare-tx-sites \
-a ${bedmethyl_a} \
-b ${bedmethyl_b} \
--out ${output.bed} \
--single-mod-code a \
--plot volcano.svg \
--gtf ${gtf} \
--log debug.log
The volcano plot requires that --single-mod-code is used, since log2 fold-change is essentially a 2-class metric.
These data were downloaded from the reference You et al., Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches
Schema of output
| column | name | description | type |
|---|---|---|---|
| 1 | chrom | name of contig from GTF | str |
| 2 | chromStart | 0-based start position | int |
| 3 | chromEnd | 0-based exclusive end position | int |
| 4 | name | modification codes present at this position | str |
| 5 | score | likelihood ration score | float |
| 6 | strand | strand, ‘+’ or ‘-’ | str |
| 7 | p_value | p-value of alternative hypothesis | float |
| 8 | gene_id | gene-id from the GTF | str |
| 9 | gene_name | gene-name from the GTF or ‘-’ if not found | str |
| 10 | log2_fold_change | log base 2 fold change | float |
| 11 | cond_a_proportions | JSON formatted string of condition ‘A’ per-modification proprotions | str |
| 12 | cond_b_proportions | JSON formatted string of condition ‘B’ per-modification proprotions | str |
| 13 | cond_a_counts | JSON formatted string of condition ‘A’ per-modification counts | str |
| 14 | cond_b_counts | JSON formatted string of condition ‘B’ per-modification counts | str |
Columns 11 through 14 are only present when the --full flag is passed.