MAGeCK count CRISPR screening

[angel]

I’m trying to upload control sgRNA file (.txt) in MAGeCK count and MAGeCK test.
After complete uploading in history, system showed that this file was unavalible in the selection list
of control sgRNA file.

I’ve tried to upload different file format (.txt/.csv/.tsv), then all of them were failed.
I do not know if anyone has experience with that problem and could help me.
Thanks a lot for the help in advance.

[jennaj]

Welcome, @angel

Tools screen for specific datatypes when accepting inputs. For this input, the tool is expecting a dataset with the tabular datatype assigned.

How to know which datatype a tool is expecting is in this topic and a few others.

@jennaj

if you are ever not sure what datatype(s) a tool accepts as input, any tool not just those that accept reads, try this:

1. Create a new empty history
2. Load up the tool form
3. Review the input datatypes listed in the tool form’s input area
4. Note: A tool could have more than one input area and this works for all user-supplied inputs from the history.

Example

Search: Search results for 'tool doesn't recognize input' - Galaxy Community Help

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Situations when the (unavailable) message can be generated

1. Dataset 72 was originally accepted by a tool run.
2. It had a tabular datatype assigned, or was drag-and-dropped.
3. The latter breaks some built-in checks – you can try this way but expect problems exactly like this.
4. Or, the first was done, but the datatype assigned to dataset 72 was modified to be something other than tabular.
   → When the “rerun” function is used to load up the tool form, it preloads what was originally input. If the metadata datatype was changed to be anything other than tabular, it won’t be accepted.

Keep in mind that none of this is about the file content. The data still needs to be in tabular format and have data in the columns it can understand.

Examples are down in the help section of the tool form. The GTN also has tutorials.
https://training.galaxyproject.org/training-material/search?query=MAGeCK

There is a training event going on all week if interested. It is not too late to join. The bonus is a dedicated chat per tutorial, and the authors and other Galaxy scientists are there to help (including me). Smörgåsbord 3: A week of Free, Online, Galaxy Training supported by the Global Galaxy Training Community

Hope that helps!

[angel]

Thanks for you helpful advice.
I choose the “Edit Dataset Attributes” icon (pencil icon) then convert the dataset from .txt to .interval, and it really work!