'Hidden' Galaxy features which are really useful /AddOrReplaceReadGroups -autoasign

Question: 'Hidden' Galaxy features which are really useful /AddOrReplaceReadGroups -autoasign

3.1 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Though I am a fairly intensive galaxy user though I had never seen an explanation of what the scratchbook was until I sawe a tweet about it a while ago. Now I could not live without. Yet even when I search the wiki I cannot find any mention of it (thought there are 2 short posts to biostar).

In case you do not know, it is activated by the little 3x3 grid symbol in the upper right corner, next the usage number. If you punch this then it goes yellow. Then every dataset eye that you punch will popup as a window allowing you easily compare multiple datasets at the same time. A really useful feature whoever implemented it. Punch the 3x3 icon again to hide the windows.

Here is my question to justify this post, I have just noticed that on my galaxy server (not usegalaxy.org) there are new options for the tool AddOrReplaceReadGroups add or replaces read group information (Galaxy Tool Version 1.136.0)(at least I think they are new).

Specifically 'autoasign' readgroup @RG , sample @SM and library @LB . I am guessing these options are taking the info from elsewhere (maybe the dataset name), which would be really really helpful.

Is there any description of the 'autoasign' option??

Thanks Guy

autoasign addorreplacereadgroups scratchbook • 1.6k views

ADD COMMENT • link •

modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

Thank you very much for this post. Scratchbook explanation is also provided here: https://vimeo.com/120839821

ADD REPLY • link written 3.1 years ago by Martin Čech ♦♦ 4.9k

Thanks Martin. The video is great all round definitely worth 10 mins.

The scratchbook basic bit starts around 1:25 for a minute. Then there is another bit about how to graph multiple datasets in the same window around 7:00 - which I will definitely use a lot now I know about it

Thanks Guy

ADD REPLY • link written 3.1 years ago by Guy Reeves • 1.0k

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Guy,

For details of automatic read group assignment, please see the first three "macros" in the code at github.

This is brand-new and could use more user documentation. Scratchbook included here: GalaxyProjectWorkshop2015

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

3.1 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

HI Jen

Thanks for the information the link to the workshop is very useful.

I had an ill-informed look at the github pages and as far as I can see the ''autoasign' options on BWA or AddOrReplaceReadGroups

will place the dataset name as @rg ID , sample SM and library LB in the Bam files if there is a single imput into the tool (this is what happens when I have tested it. If you are using data collections or there is more that one input dataset then then things get more complicated- which i have not looked at.

https://github.com/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f

There does not appear to be any capacity to parse text in the dataset name so autoasign can place different values in ID SM or LB but I may be wrong about that. But even so it is still a very useful feature in workflows.

Thanks Guy

ADD COMMENT • link written 3.1 years ago by Guy Reeves • 1.0k

Still suspect that autoasign could do with some documentation from somebody more informed than me

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

Users should note that you still need to put some text in the platform (PU) field as this is required or you will get an error (which is not directly related to a missing EOF as the first line of the error suggest )

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

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