Update ChIP-Seq tutorial with latest tool versions and links #4290
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anuprulez
reviewed
Jul 17, 2023
| @@ -306,7 +307,7 @@ Since in this tutorial we are interested in assessing H3K4me3, H3K27me3 and CTCF | |||
| > ``` | |||
| > | |||
| > 3. Rename the files | |||
| > 3. **multiBamSummary** {% icon tool %} with the following parameters | |||
| > 3. {% tool [multiBamSummary](toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0) %} with the following parameters: | |||
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Can we use the latest version of the multiBamSummary tool which is: Galaxy Version 3.5.2+galaxy0 or is there a specific reason to use one prior version?
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because this is the most common latest version on .org and .eu
anuprulez
reviewed
Jul 17, 2023
| @@ -322,7 +323,7 @@ Since in this tutorial we are interested in assessing H3K4me3, H3K27me3 and CTCF | |||
| > | |||
| > Using these parameters, the tool will take bins of 1000 bp separated by 500 bp on the chromosome X. For each bin the overlapping reads in each sample will be computed and stored into a matrix. | |||
| > | |||
| > 4. **plotCorrelation** {% icon tool %} with the following parameters | |||
| > 4. {% tool [plotCorrelation](toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0) %} with the following parameters: | |||
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Similar comment as previously made for the multiBamSummary tool, can we use the latest version?
|
I ran this tutorial on EU, and it works fine. I verified all the updated steps except for the very last plot that compares all the 8 pairs of samples (which is time-consuming). history: https://usegalaxy.eu/u/kumara/h/chip-seq-1 ping @pavanvidem |
gallardoalba
approved these changes
Jul 17, 2023
|
thanks @anuprulez @gallardoalba |
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