Up: Component summary
Up: Component summary
Component
SelectMethContextSeparate cytosines based on the methylation context in which they occur and produces statistics about context methylation.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Alignment DNA Methylation |
| Authors | Chiara Facciotto (chiara.facciotto@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml SelectMethContext.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| methCall | CSV | Mandatory | File containing the methylation percentages obtained from after the methylation calling (MethCalling function), containing a column wth the context at which methylation occurs (i.e., either CpG, CHG or CHH, where H can be A, T or C). |
Outputs| Name | Type | Description |
|---|---|---|
| cpg | CSV | CSV file containing all cytosines (methylated or not) at CpG context. |
| chg | CSV | CSV file containing all cytosines (methylated or not) at CpG context. |
| chh | CSV | CSV file containing all cytosines (methylated or not) at CpG context. |
| statistics | CSV | CSV file containing the percentage of methylation occuring at CpG, CHG and CHH context. In this case only the methylated cytosines are considered in the analysis. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| coverage | int | 10 | Minimum read coverage a cytosine needs to have in order for its methylation percentage to be considered reliable. If the coverage is under this threshold the cytosine will still appear in the the context file but it will not be used to compute the statistics. |
| methPerc | float | 0.5 | Minimum methylation percentage a cytosine needs to have in order to be considered methylated. If the methylation percentage is under this threshold the cytosine will still appear in the the context file but it will not be used to compute the statistics. The percentage is represented by values between 0 and 1. |
Test cases| Test case | Parameters▼ | IN methCall |
OUT cpg |
OUT chg |
OUT chh |
OUT statistics |
|---|---|---|---|---|---|---|
| case1_default | (missing) | methCall | cpg | chg | chh | statistics |
| case2_coverage | properties | methCall | cpg | chg | chh | statistics |
|
# Testing SelectMethContext component, |
||||||
| case3_methPerc | properties | methCall | cpg | chg | chh | statistics |
|
# Testing SelectMethContext component, |
||||||