opened
sand60
username_0
### Instructions

- Use a **concise** yet **descriptive** title;
- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request**;
- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;
- Delete the other template blocks and this header.

----

## Bug Report

### Affected tool(s)
_Tool name(s), special parameters?_

### Affected version(s)
- [ ] Latest public release version [version?]
- [ ] Latest development/master branch as of [date of test?]

### Description 
_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._

#### Steps to reproduce
_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem and provide a minimal test case._

#### Expected behavior
_Tell us what should happen_

#### Actual behavior
_Tell us what happens instead_

----

## Feature request

### Tool(s) involved
_Tool name(s), special parameters?_

### Description
_Specify whether you want a modification of an existing behavior or addition of a new capability._
_Provide **examples**, **screenshots**, where appropriate._

----

## Documentation request

### Tool(s) involved
_Tool name(s), parameters?_

### Description 
_Describe what needs to be added or modified._

----
Is picard CollectRrbsMetrics tested on WGBS, can it be used with WGBS to get reliable metrics?
issue
created
yfarjoun
username_1
Please elaborate to the differences and possible pitfalls that you are thinking about...
comment
created
sand60
username_0
Actually I was wondering how appropriately would this tool calculate whole
genome bisulfite conversion rates? Then I kind of answered myself that this
tool may be just looking at RRBS sites and since they only represent a
subset of the genome, the conversion rates reported by it are not
representative of the whole genomed. Is that a fair assumption?
Thanks for reaching out.
Best!
Sukhinder
comment
created
yfarjoun
username_1
I am no tan expert on the matter, but I do not see anything in the code that pertains to particular sites. it seem to be simply calculating the **average** conversion rate. If you the results collected per gene, or per region, you'd have to look (or write!) a different tool.
comment
created
yfarjoun
username_1
sorry. I spoke too soon. the tool will also emit **detailed** metrics that show EACH of the CpG sites it encounters and how often they were seen to be "converted"
comment
created
sand60
username_0
Thanks Yossi,
appreciate your feedback. It does mean I need to get back at those results
and probably believe them then. But I don't understand why the tool is
called CollectRrbsmetrics, because RRBS is a specific type of bisulfite
sequencing where the MspI digested DNA is treated with bisulfite. Below is
some more info, thanks for your help.

https://epigenie.com/epigenetics-research-methods-and-technology/methylcytosine-5mc-analysis/bisulfite-conversion/rrbs-reduced-representation-bisulfite-sequencing/

best!
comment
created
sand60
username_0
Hi Broadinstitute/Picard,
May I please know why would my Picard RRBS summary file have negative
values for
NON_CPG_BASES  && NON_CPG_CONVERTED_BASES .
Attached is an output. Thank you so much for your attention.

On Wed, Apr 24, 2019 at 12:42 PM Sukhinder Sandhu <sukhdeol07@gmail.com>
wrote:

> Thanks Yossi,
> appreciate your feedback. It does mean I need to get back at those results
> and probably believe them then. But I don't understand why the tool is
> called CollectRrbsmetrics, because RRBS is a specific type of bisulfite
> sequencing where the MspI digested DNA is treated with bisulfite. Below is
> some more info, thanks for your help.
>
>
> https://epigenie.com/epigenetics-research-methods-and-technology/methylcytosine-5mc-analysis/bisulfite-conversion/rrbs-reduced-representation-bisulfite-sequencing/
>
> best!
>
>
comment
created
yfarjoun
username_1
this seems to be a new, unrelated issue. please start a new issue with your question (or even better, ask it on the GATK forum https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum)
comment