IF YOU REVIEW ADD YOUR ISSUES HERE

[strambc]

Please enter any comments you have on the revised version of the FOF-CT on ReadTheDoc (https://fish-omics-format.readthedocs.io/en/update_docs_caterina_rahi/index.html#)
as a comment on this issue.

[SarahAufmkolk]

Minor comments - location is given first, then the text element that is commented on, then the suggestion:

FOF-CT: Chromatin Tracing

• Introduction
o Background
 FISH Omics techniques description

• …and their location in individual cells can be imaged using either traditional microscopy techniques (e.g., widefield or confocal)or super-resolution microscopy as reviewed by (Fraser et al.) and (Jerkovic and Cavilli) --> space after bracket is missing. Punctuation missing in the end.

• As a logical evolution of more traditional techniques allow the detection of multiple and ideally all DNA locations across the genome. (unclear) --> Suggestion: Evolutions of these techniques expanded the number of imaged targets to multiple and potentially all DNA locations across the genome.

• Example

• Tip: the Optional columns in this exam --> The optional columns…

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Addressed in commit on 9/10/2024

[RahiNav]

• The tip section on format overview "If included all Tables, except DNA-Spot/Trace Data core table, Spot Demultiplexing table, RNA Spot Data table and Cell/ROI Mapping table, MUST contain at least 1 Optional Column." is not very clear, maybe rephrase?
• Should we add a link to a dataset which have different FOF-CT tables from 4DN under downloadable template? It may help user understand how the tables look like with real data.
• In the example with insertion/deletion, maybe we should include a note that an additional file in vcf format is required along with the actual tables. It may not be obvious to users even though it is mentioned in the headers.
• I think the tip which talks about "4DN Data Portal only accepts GRCh38 for human and...." should be moved under the tables section and under downloadable templates section. Right now it is place under the core table, so may not be that obvious.

@RahiNav, what do you mean by this? Should we create another section?

• My opinion: I think we should move the tables section under the main menu as a separate page like tables overview rather than a sub-heading. I think it will be easy to find and more helpful for the users.

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Fixed all indicated in commits on 9/13/2024

[SarahAufmkolk]

• I agree with Rahi about giving the tables section its own headline (I found myself searching for it several times.)

• In this context, can we add in each tab the Namespace as well? Example:

Trace Data table
Requirement level: optional
Recommended: Yes
Namespace: 4dn_FOF-CT_trace

Minor revisions:

• File Header
  #Intensity_Measurement_Method:

If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts. --> *perform and counts

• Example

Tip:
the Optional columns in this example table are included for illustrative purposes only and describe a case in which DNA spots are detected with multiplexed barcodes.  The optional

• Example
  Tip: the Optional columns in this exam  The optional columns…

• File Header
  The header MUST contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. In case more than one algorithm were used, please use the same set of fields for each of them.  If more than one algorithm was used…
   I would understand that if the user used eg two software we would have the following situation for the header:

#Software_Title:

The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.

ChrTracer3

#Software_Type:

The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other

SpotLoc+Tracing

#Software_Title:

The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.

Software_B

#Software_Type:

The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other

QC with Software B

The first column entry like Software_Type would be the same for both Software, correct? Or would the user have to number the entry: like # Software_Type002
I assume the first suggestion is true, in which case the text is clear.

• Example
  Tip:
  the Optional columns...

• Example

…as described in Doe et al., 20221. --> even if this is a fictional reference, I assume that it should be 2021 as in the fictional paper below.

• Data Columns
  Trace_ID
  This fields reports the unique identifier for a DNA Trace identified as part of this experiment. Note: this is used to connect data in this table with a given Trace and with Trace specific measurements as recorded in the corresponding Trace Data table.  This field…
  Is DNA Trace used deliberately here or should it be RNA trace? Since the Trace table is used for the DNA traces aswell, we should clarify that more. Maybe even start counting at Trace_ID 3 since we used 1, 2 in the DNA example on the DNA-Spot tab.
  1  In the example below 001 is used as Trace_ID  Should we write an integer in the example below, since we used it in other tabs as well.

[strambc]

• Finish Template page
• Add links to Template table for each table type
• Ceck internal consistency of example tables