DESeq2 settings for FeatureCounts input; Compute versus Filter functions

error
deseq2
featurecounts
filter
compute

#1

im doing an rna seq analyses and saw 2 error today
1 : when i use feature counts then i cant use Deseq2 . if you use feature counts you cant use Deseq2. i tried everything but it didnt work.
2: in compute tool, no matter what your script is, if you use “bool” command, it does not working .
im be appreciate if anyone can help me


#2

Hello, Sorry you are having trouble! It is difficult to diagnose the problem without more information.

Are you working at Galaxy Main https://usegalaxy.org? If so, please consider sending in a bug report from one of the error datasets. Leave all error/input datasets in the history undeleted. In the bug report comments, you can include a link to this post for cross-reference.

Click on the green “bug” icon in a red error dataset to bring up the bug reporting form.

More about how to submit a bug report: https://galaxyproject.org/support/tool-error/#determining-the-job-failure-type

Or, you can try to compare your methods to those in our tutorials first to troubleshoot. This is a basic introduction that covers FeatureCounts and DESeq2:

There are a few “compute” tools, so I’m not quite sure which you are using, but if that is in the same history with the other problems, we can review it at the same time. If in a different history, please also send a bug report from that error.

Let’s start there, thanks!


#3

Update: I found your histories with the errors.

Compute:

  • Use the Filter tool instead of Compute.
  • Remove the explicit “bool”, “true”, “false” content from the expression. How to construct expressions is explained on the tool form.
  • If you want to publically share a specific example you are having trouble with (the filter expression + a few data lines it should act on true/false), we can help with formatting back here. Or, you can submit the error as a bug report for help.

DESeq2:

  • The FeatureCounts inputs have a header but the option “Files have header?” was set to “No”.
  • Change that to “Yes” and try a rerun.
  • I didn’t notice any other obvious issues and that will solve the current failure reason.

#4

thanks for your attention. it was a big help.


#5

but if i use filter tool, it does not give me the true/false things. tru/false option which i need for goseq, only comes from compute tool


#6

Yes, for that usage, “bool” can be used in a Compute expression – but that is usually optional for many use cases – and importantly, it only works in the newer tool version (1.2.0) as sourced from the ToolShed.

The GTN Tutorial that covers this usage and you appear to be referencing, is noted for only working at the Galaxy EU https://usegalaxy.eu public server (it includes versions of the tool that work with “bool” expressions).

We just now updated Galaxy Main https://usegalaxy.org to include the tool Compute an expression on every row (Galaxy Version 1.2.0).

The installation is not finalized yet – so when clicking on the tool from the tool panel, the older version (1.1.0) will be loaded. Use the “Versions” menu at the top of the tool form to switch the version to 1.2.0. The “rerun” button on a formerly failed dataset resulting from the older version will prompt with a redirect to the newer version. These details will be sorted out shortly – but you can use the newer tool now.

Your expression queries did have some other format problems – it is hard to tell which were actually wanted and which were just tests after the failures. Please carefully review the help on the newer 1.2.0 tool form – it should help clarify how to format expressions plus includes a listing of all the supported functions. If you cannot get it right, post the expression back here and we can help.


#7

Here is an example of Filter versus Compute for a complex expression.

Input tabular dataset:

chrH    3       10      -1
chrI    5       12      1
chrJ    7       14      -1
chrK    11      16      1

Result from Filter with the expression: (c2<7 and abs(c4)>=1)

chrH    3       10      -1
chrI    5       12      1

Result from Compute with the expression: (c2<7 and abs(c4)>=1)

chrH    3       10      -1      True
chrI    5       12      1       True
chrJ    7       14      -1      False
chrK    11      16      1       False

#8

So… what should i do? is there any way to do this exact function with “Filter” or should i download some thing or else ??


#9

You can use the Compute tool now the same as in the tutorial, or construct your own query if you want the True/False output from it. Just be sure to use the updated version of the tool if including a bool() function explicitly in the expression (even though that is probably not needed, as in the example above for:


#10

how can i upgrade the tool in galaxy ?


#11

It has already been updated at Galaxy Main https://usegalaxy.org. Are you working somewhere else now?


#12

thats why im asking that question. im working at usegalaxy.org too. so it must been updated. but i still have this problem . thats where im confusing right now


#13

Do you want to share your Compute query? There might be a syntax problem.

Or, you might still be using the older version of the tool. Open up the form and look at the top, you want to use Compute an expression on every row (Galaxy Version 1.2.0). If still using 1.1.0, use the “Versions” button at the top to switch to the newer version (for a direct run) or swap the tool out to the newer version (for a workflow).


#14

its 1.2.0. im even sending you my data to look out.maybe some things wrong in my data.
every things are workings in Compte except bool command .

maybe we should share it publicly to see anyone else maybe notice that and actually solve it


#15

Hi - The expression c3-c2 is a computation that subtracts the value in column 2 from the value in column 3. The result will be a new dataset, containing all the columns of the original input dataset plus that result added as a new column at the end of each row.

If you want a True/False result instead from Compute, then the expression needs to compare/compute values. Example: c3>=c2

Help from the tool form: