Open shiltemann opened 5 years ago
shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Network analysis with Heinz (Transcriptomics)
How did you use this tutorial?: At a workshop.
Usefulness: 5
Quality: 5
Length: Perfect
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?:
What did you like?:
What could be improved?: maybe some interpretation of the results. ie what genes are involbved, what might this mean? The tutorial mentions that this can be done, but some more discussion of what would be done with the resulting optimal subnetwrk would help pull it all together.
Please provide any feedback you have on your experience with this tutorial.:
Do you have suggestions for additional topics or tutorials?:
Your institution:
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 3
What did you like?: It was well structured and simply explained
What could be improved?: It would be very helpful if the parameter setting on the tools was discussed a bit more and explain the reason why to certain choices
Tutorial: Network analysis with Heinz (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Topic and clarity (DIY is easy)
What could be improved?:
Tutorial: Network analysis with Heinz (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Nice clear and good to start a bit further down for speed so it fits the program.
What could be improved?: note that the use of build list is unclear, perhaps good to move description of how to solve this up so to prevent questions.
Tutorial: Network analysis with Heinz (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: step by step manual
What could be improved?: it is good enough
Tutorial: Network analysis with Heinz (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Easy to follow and understand
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Easy to follow with great pictures and arrows and labels
What could be improved?: none
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Detailed explanation with screenshots!
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Intuitive and well executed. Images were useful in following the flow of the tutorial.
What could be improved?: There is no answer to the question under the section entitled 'Re-run that tool with changed settings'. A 'Done' button does not appear in the view history screen as well.
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: explorations, explanations
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 3
What did you like?: Clarity and background details
What could be improved?: Need a step on how to remove barcodes, adapters and primers from raw FASTAq sequences
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Topic and completeness of the scope
What could be improved?: I think there is an error: Join two Datasets tool
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Very very straightforward !
What could be improved?: Nothing...
Tutorial: Running the Galaxy Training material website locally (Contributing to the Galaxy Training Material)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: RNA-seq counts to genes and pathways (Transcriptomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
Tutorial: Calling variants in diploid systems (Variant Analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 2
What did you like?: Krona
What could be improved?: It needs to be updated, some returns error and some is missing. Be more detail and specific
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: "Easiness",
What could be improved?: You could link to short description of what a fastq format is, etc... and warn that Filterbyquality sometimes is not present. I could not find it. I use FilterFASTQ instead
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 1
What did you like?: Some instructions were not clear at all, please be more specific as i encounter errors very likely despite following the steps
What could be improved?: Please review the protocol and revise some segments
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: It's easy to follow.
What could be improved?: For clean Ubuntu 18.04 Ansible couldn't find python (it was not installed, weird), so it crashed. There should be rule added to check and install python if it is not installed. Refer to this solution - https://gist.github.com/gwillem/4ba393dceb55e5ae276a87300f6b8e6f.
Tutorial: Ansible (Galaxy Server administration)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Mapping (Sequence analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: all of it!
What could be improved?: how to rmemeber steps....
Tutorial: Quality Control (Sequence analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: This made using Galaxy very simple.
What could be improved?: This should be the first tutorial that shows up, even before the longer version as now I would feel more comfortable doing the long one whereas that one was overwhelming at first.
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: excellent intro, thanks!
What could be improved?:
Tutorial: Ansible (Galaxy Server administration)
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received (extended form)
Which GTN tutorial did you complete?: NGS data logistics (Introduction to Galaxy Analyses)
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 5
Quality: 5
Length: Perfect
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?: I myself is a student
What did you like?: Everything about the tutorial. It was so clear and easy to understand along with practical demonstration. I feel it is a complete package to learn NGS from scratch
What could be improved?: Please add the next steps or the separate tutorial like this on Chip-Seq data. I am interested to work after Alignment steps, that starts from Peak calling.
Please provide any feedback you have on your experience with this tutorial.: Excellent. I learned at great deal
Do you have suggestions for additional topics or tutorials?: Yes, please make a detail tutorial on Chip-Seq data analysis from scratch to final steps (peak visualization and how do we analyze that). or if you already have that tutorial pls give a link for it
Your institution: Indiana State University, US
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?: One could add a section describing the use of multiple datasets, tags, etc.
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 1
What did you like?: I like the idea of it
What could be improved?: It seems impossible to complete. The training data is not available in the shared data link. If it is, it's too hard to find. A more general point would be to explain how the tutorial could be used on other data sets. or ref genomes. For this I tried using an hg19 fasta file from another data set, but got an error about indexing. So I guess, explaining how the training data sets are pre-formatted would help when trying to use sets from other sources
Tutorial: Exome sequencing data analysis (Variant Analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 2
What did you like?:
What could be improved?: I'm still in the middle of it. But when doing snpEFF there is no refernece genome available. This tutorial does not say to download one. Other variant analyses say to download hg19. this is not available in the shared data folders. When using an hg19 fasta from another source freeBayes fails because it isn't indexed. Not sure how to index it. SnpEFF calls for a database. I downloaded one and am trying it now. But it would be good to include this step in the tutorial
Tutorial: Calling variants in diploid systems (Variant Analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 2
What did you like?: I like the idea
What could be improved?: After running the FreeBayes I ended up with 2 variants instead of 30. And so got stuck there. Also it's not clear why the filtering and subsequent steps would be done on the markduplicates output, rather than the left align output. Why do the leftalign if we don't use that output again? I did both and got the same results. Overall I am finding the galaxy experience to be rather frustrating. I'm trying to decide whether to incorporate these tutorials in my class, but often I can't find the necessary input data, get unexplained errors, or get output different from the tutorial
Tutorial: Calling variants in non-diploid systems (Variant Analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: This was very straight forward and ran well (once it was clear that it only runs on the eu site). listing the file types was useful
What could be improved?: maybe link to descriptions of the various file type generated/used
Tutorial: Microbial Variant Calling (Variant Analysis)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Introduction to Genome Assembly (Assembly)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: IGV Introduction (Introduction to Galaxy Analyses)
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shiltemann
commented
5 years ago New GTN feedback received (extended form)
Which GTN tutorial did you complete?: IGV Introduction (Introduction to Galaxy Analyses)
How did you use this tutorial?: I took the tutorial on my own.,To teach a workshop.
Usefulness: 4
Quality: 4
Length: Too short
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?: 10
What did you like?: Image wise explanation on using a particular tool.
What could be improved?: More content according to case studies and some video output as well.
Please provide any feedback you have on your experience with this tutorial.: Very nicely presented the data, just the content addition needs to be little more; showing examples relatively till data interpretation with conclusion & future aspects as well.
Do you have suggestions for additional topics or tutorials?: Metagenomic Data Analysis with visualization tutorial how to upload, view and data interpretation; other than that, 5C-Seq Analysis, RIP-Seq Analysis, Mnase-Seq Analysis and FAIRE-Seq Analysis should also be available including few interesting topics like ribosome profiling, epigenomic sequencing, miRNA/ncRNA sequencing data analysis.
Your institution: RASA Life Science Informatics, Pune, Maharashtra, India.
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: The overview of all the tools available.
What could be improved?: The time for the processes on Galaxy.
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: clear step by step module
What could be improved?:
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Thorough step by step directions. Does not assume you know stuff already.
What could be improved?: Naming the output files was a little confusing, especially when I was left on my own to continue to name all the rest of them. Why doesn't the new name show up in the workflow boxes after you name them?
Tutorial: Workflows: Extracting Workflows from Histories (User Interface and Features)
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shiltemann
commented
5 years ago New GTN feedback received
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Clear and consise
What could be improved?: N/A
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Simplicity
What could be improved?: Nothing
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: easy to follow individual steps
What could be improved?: Chipseq data seems a little more complex than more 1-dimensional seq reads (DNA/RNAseq), so would seem to me that starting with e.g. RNAseq analysis could be more logical
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?: Easy to follow tutorial
What could be improved?: We did not realize the 00000000rik names were also gene names, so we spent some time thinking we did something wrong...
Note: this comment was autogenerated
shiltemann
commented
5 years ago New GTN feedback received
Tutorial: Mapping (Sequence analysis)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated
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