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- Complete either the corrected Samtools Tutorial, or the abbreviated cook-book-version. (The cookbook version is worth looking at even if you complete the full tutorial as it teaches another way of executing the same commands)
- Go back to the IGV tutorial, look through the E. coli section with particular regard to loading IGV, but don't delay or look too in depth there.
- Focus more on the 2nd set of data: Humans.
- Copy the human data over to $SCRATCH before the presentation starts to make sure it is available after our break.
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cds mkdir BDIB_Human_tutorial cp -r $BI/ngs_course/human_variation BDIB_Human_tutorial/raw_files & # This command will take some amount of time to finish. Move onto the next task while you wait, and later when it has finished copying do the next command cd $SCRATCH/BDIB_Human_tutorial/rawfilesraw_files gunzip *.gz # this will unzip all the compressed files you have just copied |
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Either method is fine, but you should look at the abbreviated version as it introduces a new type of command execution:
Step 4: IGV
Go through the IGV tutorial paying special attention to how to load IGV on your local computer and the 2nd set of data covering human information.
Yesterday we went through how to launch IGV on your local computer (IGV tutorial).
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| Cheatsheet of what to do. |
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| title | In IGV, use "file -> load from URL" to open each of the following URLs |
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We will now proceed with the presentation, and hopefully the copy will finish during that.