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| == Setup in person at the SeqShop Workshop == | | == Setup in person at the SeqShop Workshop == |
| ''This section is specifically for the SeqShop Workshop computers.'' | | ''This section is specifically for the SeqShop Workshop computers.'' |
− | <div class="mw-collapsible mw-collapsed" style="width:600px"> | + | <div class="mw-collapsible" style="width:600px"> |
| ''If you are not running during the SeqShop Workshop, please skip this section.'' | | ''If you are not running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| == Setup when running on your own outside of the SeqShop Workshop == | | == Setup when running on your own outside of the SeqShop Workshop == |
| ''This section is specifically for running on your own outside of the SeqShop Workshop.'' | | ''This section is specifically for running on your own outside of the SeqShop Workshop.'' |
− | <div class="mw-collapsible" style="width:600px"> | + | <div class="mw-collapsible mw-collapsed" style="width:600px"> |
| ''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"> |
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− | This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] | + | This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, December 2014|Alignment Tutorial]] |
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− | It also uses the bam.index file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]] | + | It also uses the bam.list file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, December 2014#GotCloud_BAM_List_File|GotCloud BAM List File]] |
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| * BAMs->INDELs rather than BAMs->SNPs | | * BAMs->INDELs rather than BAMs->SNPs |
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− | If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]] | + | If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, December 2014#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]] |
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| == Running GotCloud Indel == | | == Running GotCloud Indel == |