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| + | '''Note:''' the latest version of this practical is available at: [[SeqShop: Sequence Mapping and Assembly Practical]] |
| + | * The ones here is the original one from the June workshop (updated to be run from elsewhere) |
| + | |
| == Introduction == | | == Introduction == |
| See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial. | | See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial. |
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| ''If you are running during the SeqShop Workshop, please skip this section.'' | | ''If you are running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | === Download the example data === | + | === Download & Build GotCloud === |
| + | If you do not already have GotCloud: |
| + | * cd to where you want GotCloud installed (you can change this to any directory you want) |
| + | mkdir -p ~/seqshop |
| + | cd ~/seqshop/ |
| + | * download, decompress, and build the version of gotcloud that was tested with this tutorial: |
| + | wget https://github.com/statgen/gotcloud/archive/gotcloud.workshop.tar.gz |
| + | tar xvf gotcloud.workshop.tar.gz |
| + | mv gotcloud-gotcloud.workshop gotcloud |
| + | cd gotcloud/src |
| + | make |
| + | cd ../.. |
| | | |
− | === Setup your run environment ===
| + | Remember the path to gotcloud/ that is what you will need to set your GC variable to. |
| | | |
− | Environment variables will be used throughout the tutorial.
| + | === Download the example data === |
− | | + | Download and untar file containing the example data used in the practicals: |
− | We recommend that you setup these variables so you won't have to modify every command in the tutorial.
| + | wget http://csg.sph.umich.edu//mktrost/seqshopExample.tar.gz |
| + | tar xvf seqshopExample.tar.gz |
| | | |
| + | You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file. |
| | | |
− | <div class="mw-collapsible mw-collapsed" style="width:500px">
| + | {{SeqShopRemoteEnv}} |
− | I'm using bash (replace the paths below with the appropriate paths):
| |
− | <div class="mw-collapsible-content">
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− | * Point to where you installed GotCloud
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− | *:<pre>export GC=/home/username/gotcloud</pre>
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− | * Point to where you installed the seqshop files
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− | *:<pre>export SS=/home/username/seqshop/</pre>
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− | * Point to where you want the output to go
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− | *:<pre>export OUT=/home/username/seqshop_output/</pre>
| |
− | </div>
| |
− | </div>
| |
− | | |
− | <div class="mw-collapsible mw-collapsed" style="width:500px">
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− | I'm using tcsh (replace the paths below with the appropriate paths):
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− | <div class="mw-collapsible-content">
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− | * Point to where you installed GotCloud
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− | *:<pre>setenv GC /home/username/gotcloud</pre>
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− | * Point to where you installed the seqshop files
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− | *:<pre>setenv SS /home/username/seqshop/</pre>
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− | * Point to where you want the output to go
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− | *:<pre>setenv OUT /home/username/seqshop_output/</pre>
| |
− | </div>
| |
− | </div>
| |
− | | |
− | </div>
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− | </div>
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| | | |
| == Examining [[GotCloud]] Align Input Files == | | == Examining [[GotCloud]] Align Input Files == |
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| <li>View Screenshot</li> | | <li>View Screenshot</li> |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | [[File:RefDir.png|500px]] | + | [[File:RefDir.png|700px]] |
| </div> | | </div> |
| </div> | | </div> |
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| <li>Need a reminder of the format?</li> | | <li>Need a reminder of the format?</li> |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | [[File:fqindex.png|650px]] | + | [[File:fqindex.png|750px]] |
| </div> | | </div> |
| </div> | | </div> |
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| <li>HG00553 & HG00640</li> | | <li>HG00553 & HG00640</li> |
| <li>They have multiple unique values in the RGID field</li> | | <li>They have multiple unique values in the RGID field</li> |
− | [[File:fqindexRG.png|650px]] | + | [[File:fqindexRG.png|800px]] |
| </div> | | </div> |
| </div> | | </div> |
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| | | |
| Let's look at the configuration file I created for this test: | | Let's look at the configuration file I created for this test: |
− | more ${IN}/gotcloud.conf | + | more ${SS}/gotcloud.conf |
| | | |
| Use the <code>space bar</code> to advance if the whole file isn't displayed. | | Use the <code>space bar</code> to advance if the whole file isn't displayed. |
| | | |
− | ; If your input and references are at different paths than specified, what would you change? | + | ; If your references are in a different path than what is specified, what would you change? |
| <ul> | | <ul> |
− | <div class="mw-collapsible mw-collapsed" style="width:200px"> | + | <div class="mw-collapsible mw-collapsed" style="width:300px"> |
| <li>Answer:</li> | | <li>Answer:</li> |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| <ul> | | <ul> |
− | <li>You would change <code>IN_DIR</code> & <code>REF_DIR</code> to the new paths</li> | + | <li>You would change <code>REF_DIR</code> to the new path</li> |
− | [[File:gcConf.png|500px]] | + | [[File:gcConf.png|800px]] |
| </div> | | </div> |
| </div> | | </div> |
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| | | |
| Now that we have all of our input files, we need just a simple command to run them | | Now that we have all of our input files, we need just a simple command to run them |
− | ${GC}/gotcloud align --conf ${IN}/gotcloud.conf --numcs 2 | + | ${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numcs 2 --base_prefix ${SS} --outdir ${OUT} |
| + | |
| + | * <code>${GC}/gotcloud</code> runs GotCloud |
| + | * <code>align</code> tells GotCloud you want to run the alignment pipeline. |
| + | * <code>--conf</code> tells GotCloud the name of the configuration file to use. |
| + | ** The configuration for this test was downloaded with the seqshop input files. |
| * <code>--numcs</code> means to run 2 samples at a time. | | * <code>--numcs</code> means to run 2 samples at a time. |
− | ** How many you can run concurrently depends on your system | + | ** How many you can run concurrently depends on your system. |
| + | * <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths. |
| + | ** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS} |
| + | ** Alternatively, gotcloud.conf could be updated to specify the full paths |
| + | * <code>--out_dir</code> tells GotCloud where to write the output. |
| + | ** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line |
| + | |
| [[File:gcalignStart.png|850px]] | | [[File:gcalignStart.png|850px]] |
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| [[File:Qplotpdf.png|400px]] | | [[File:Qplotpdf.png|400px]] |
| <li> Look at the PDF I produced when I ran the whole genome:</li> | | <li> Look at the PDF I produced when I ran the whole genome:</li> |
− | evince ${IN}/example/HG00551.wg.qplot.pdf& | + | evince ${SS}/ext/HG00551.wg.qplot.pdf& |
| </ul> | | </ul> |
| [[File:Qplotpdfwg.png|400px]] | | [[File:Qplotpdfwg.png|400px]] |
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| | | |
| Let's visualize what reads in that area look like using samtools tview: | | Let's visualize what reads in that area look like using samtools tview: |
− | ${GC}/bin/samtools tview ${OUT}/bams/HG00551.recal.bam ${REF}/human.g1k.v37.chr22.fa | + | ${GC}/bin/samtools tview ${OUT}/bams/HG00551.recal.bam ${SS}/ref22/human.g1k.v37.chr22.fa |
| * Type ‘g’ | | * Type ‘g’ |
| ** Type 22:36907000 | | ** Type 22:36907000 |
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| | | |
| == Logging Off == | | == Logging Off == |
| + | |
| + | ''This section is specifically for the SeqShop Workshop computers.'' |
| + | <div class="mw-collapsible mw-collapsed" style="width:600px"> |
| + | ''If you are not running during the SeqShop Workshop, please skip this section.'' |
| + | <div class="mw-collapsible-content"> |
| To logout of seqshop-server, type: | | To logout of seqshop-server, type: |
| exit | | exit |
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| | | |
| When done, log out of the Windows machine. | | When done, log out of the Windows machine. |
− | | + | </div> |
− | | + | </div> |
− | == Please provide feedback from Day 1 ==
| |
− | https://docs.google.com/a/umich.edu/forms/d/1afGq98QToC17CO8k6tXXyybIZFFfNsy8mOX5Tzc2QyM/viewform
| |