Tutorial Feedback

[shiltemann]

This issue will collect all feedback submitted via the feedback form at the end of each tutorial

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Results have been aggregated and pro/cons per tutorial

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (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]

New GTN feedback received

Tutorial: NGS data logistics (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: The explanation is very clear and concise, thanks!

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: Easy to follow

What could be improved?: Including some assignment or home work

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received (extended form)

Which GTN tutorial did you complete?: Differential abundance testing of small RNAs (Transcriptomics)

How did you use this tutorial?: I took the tutorial on my own.

Usefulness: 4

Quality: 2

Length: Perfect

Level of detail: Not enough details

If you used this material to teach, how many students/participants attended?:

What did you like?:

What could be improved?: Clarity of the files

Please provide any feedback you have on your experience with this tutorial.: Input of the given blank/simplekin files did not align to the expected outputs shown in the tutorial. For example, running a FASTQC report on the blank_rep1 did not detect Illumina universal adaptors featured in the screen shot example on your tutorial. I am unsure whether the files have been changed since the tutorial has initially made. Using the last tool DeSeq2 would not work despite following instructions very carefully. I am unsure what the final output of this tutorial is meant to be.

Do you have suggestions for additional topics or tutorials?:

Your institution:

Note: this comment was autogenerated

[shiltemann]

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]

New GTN feedback received

Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: Easy to follow, but the task is not trivial!

What could be improved?: update some of the options and screenshots to be consistent with the latest version of Galaxy

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (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]

New GTN feedback received

Tutorial: Galaxy 101 (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]

New GTN feedback received (extended form)

Which GTN tutorial did you complete?: Reference-based RNA-Seq data analysis (Transcriptomics)

How did you use this tutorial?: I took the tutorial on my own.

Usefulness: 4

Quality: 4

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?: bool function with compute option is NOT working for some reasons. I could not obtain True/False result from DESeq result file.

Please provide any feedback you have on your experience with this tutorial.: bool function with compute option is NOT working for some reasons. I could not obtain True/False result from DESeq result file.

Do you have suggestions for additional topics or tutorials?: Please include a tutorial for human genome

Your institution:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)

How much did you like this tutorial?: 4

What did you like?: The explanations and solutions to check our output

What could be improved?: Explanations of the plots

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)

How much did you like this tutorial?: 4

What did you like?: step-by-step configuration

What could be improved?: colors to enhance instructions clarity

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Visualization of RNA-Seq results with CummeRbund (Transcriptomics)

How much did you like this tutorial?: 1

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Introduction to Genome Assembly (Assembly)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Peptide and Protein ID using SearchGUI and PeptideShaker (Proteomics)

How much did you like this tutorial?: 4

What did you like?: Tutorial is absolutely awesome! Thaks a lot for the work you made!

What could be improved?: Maybe you could make the tutorial more detailed. Write all the commands exactly as they should be written in the terminal. I catch lots of failures and can't improve them by myself.(

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Quality Control (Sequence analysis)

How much did you like this tutorial?: 4

What did you like?: Nice explanation, really easy!

What could be improved?: what is the next step?

Note: this comment was autogenerated

[shiltemann]

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]

New GTN feedback received

Tutorial: Deploying a compute cluster in OpenStack via Terraform (Galaxy Server administration)

How much did you like this tutorial?: 5

What did you like?: Really detailed, could use it for my project for creating my project

What could be improved?: maybe go deeper and show a template for a project

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received (extended form)

Which GTN tutorial did you complete?: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)

How did you use this tutorial?: As an assignment for a class.

Usefulness: 5

Quality: 5

Length: Perfect

Level of detail: Too many details

If you used this material to teach, how many students/participants attended?:

What did you like?: How many transcripts have a significant change in expression between these conditions? To filter, use “c7<0.05”. And we get 249 transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states.

Please check if your answer is correct? Are you using a P value of 0.5 and not 0.05?

What could be improved?:

Please provide any feedback you have on your experience with this tutorial.:

Do you have suggestions for additional topics or tutorials?:

Your institution: Johns Hopkins

Note: this comment was autogenerated

[shiltemann]

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]

New GTN feedback received

Tutorial: Exome sequencing data analysis (Variant Analysis)

How much did you like this tutorial?: 1

What did you like?:

What could be improved?: unfortunately in compare with others tutorial, this is very unclear and o'm not satisfied please improve this very important tutorial with clear and accurate dive.

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (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]

New GTN feedback received

Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)

How much did you like this tutorial?: 5

What did you like?: Nothing :)

What could be improved?: I think it's already good and clear as it is

Note: this comment was autogenerated

[shiltemann]

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?: Step by step introduction and repetition of features

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)

How much did you like this tutorial?: 3

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

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]

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]

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?: No ambiguity and it showed some basics. Liked the labelled images.

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?: Galaxy at usegalaxy.org ends up showing "the white screen of death" extremely often (10s of times during following this tutorial).

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: IGV Introduction (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 1

What did you like?:

What could be improved?: Actually show some use-cases (there is only one and i am unable to load ENCODE data)

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Workflows: Extracting Workflows from Histories (User Interface and Features)

How much did you like this tutorial?: 4

What did you like?:

What could be improved?: Galaxy does not run the last step of the workflow (concatenate forward and reverse overlaps) - does not even appear in the history at all

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Introduction to Genomics and Galaxy (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 4

What did you like?:

What could be improved?: Galaxy says it has ran the workflow, but nothing happens.

Note: this comment was autogenerated

[shiltemann]

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?: Easy to follow and use

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: NGS data logistics (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: Explanation of theoretical basics. Links to additional resources.

What could be improved?: Mark Duplicates step fails:

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/022/055/22055178/_job_tmp -Xmx7g -Xms256m 11:37:37.876 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/picard-2.18.2-py36_0/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jan 17 11:37:37 CST 2019] MarkDuplicates INPUT=[Filter_on_data_7__Filtered_BAM] OUTPUT=/galaxy-repl/main/files/029/341/dataset_29341054.dat METRICS_FILE=/galaxy-repl/main/files/029/341/dataset_29341053.dat REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Thu Jan 17 11:37:37 CST 2019] Executing as g2main@roundup55.tacc.utexas.edu on Linux 3.10.0-693.21.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.2-SNAPSHOT INFO 2019-01-17 11:37:38 MarkDuplicates Start of doWork freeMemory: 248936480; totalMemory: 259588096; maxMemory: 7265714176 INFO 2019-01-17 11:37:38 MarkDuplicates Reading input file and constructing read end information. INFO 2019-01-17 11:37:38 MarkDuplicates Will retain up to 26325051 data points before spilling to disk. [Thu Jan 17 11:37:38 CST 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=382373888 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 262, Read name M01368:16:000000000-A3M99:1:2114:3862:13382, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:495) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:232) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Deploying a compute cluster in OpenStack via Terraform (Galaxy Server administration)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: NGS data logistics (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: awesome and answered many of the questions in my head

What could be improved?: nothing I can think of

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Quality Control (Sequence analysis)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 4

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

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]

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?: Images with arrows, and short answer questions (made sure I was on the right path). The icons in the text were also a nice touch.

What could be improved?: I found the boxes around each of the big steps a little distracting. They are not necessary for the transition between the steps. The large headings are enough.

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Quality Control (Sequence analysis)

How much did you like this tutorial?: 2

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Age prediction using machine learning (Statistics and machine learning)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy Tool Management (Galaxy Server administration)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy Installation with Ansible (Galaxy Server administration)

How much did you like this tutorial?: 5

What did you like?:

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

New GTN feedback received

Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)

How much did you like this tutorial?: 5

What did you like?: Very good explanations, good demonstration of Galaxy potential for begginer

What could be improved?:

Note: this comment was autogenerated

[shiltemann]

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