Difference between revisions of "Stacks"
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Widely-used Radseq analysis software protocol by Julian Catchen. | Widely-used Radseq analysis software protocol by Julian Catchen. | ||
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| + | =Stages= | ||
| + | |||
| + | == Overall == | ||
| + | |||
| + | There are 5 stages: | ||
| + | |||
| + | * Reads are demultiplexed and cleaned by '''process_radtags'''. | ||
| + | * Loci must be built with '''ustacks''' (if de-nov/no-reference) or '''pstacks''' (if with reference) | ||
| + | * Creating the catalog of loci '''cstacks''' | ||
| + | * Matching against catalog with '''sstacks'''. | ||
| + | * Either the '''populations''' or '''genotypes''' program is executed, depending on input datasets, | ||
| + | |||
| + | == setting up database on mysql == | ||
* Create database, you must have the appropriate privileges for this. If you do, the command will be something like: | * Create database, you must have the appropriate privileges for this. If you do, the command will be something like: | ||
echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p | echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p | ||
Revision as of 16:52, 19 April 2016
Widely-used Radseq analysis software protocol by Julian Catchen.
Stages
Overall
There are 5 stages:
- Reads are demultiplexed and cleaned by process_radtags.
- Loci must be built with ustacks (if de-nov/no-reference) or pstacks (if with reference)
- Creating the catalog of loci cstacks
- Matching against catalog with sstacks.
- Either the populations or genotypes program is executed, depending on input datasets,
setting up database on mysql
- Create database, you must have the appropriate privileges for this. If you do, the command will be something like:
echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p
- Ensure $STACKSROOTDIR/share/stacks/sql/my.cnf is set up properly
- Ensure modification privileges for the user
- Load stack.sql schema onto the database. It's in $STACKSROOTDIR/share/stacks/sql/stacks.sql, i.e.
mysql <mydbname> -h <name_of_server_running_mysql> -u <myusername> -p < $STACKSROOTDIR/share/stacks/sql/stacks.sql
- For whatever reason one can also start over by deleting a database. Care should be taken with a step like this, just in case one deletes the wrong database. The delete command's keyword is in fact "DROP" and woudl be run like this:
echo "DROP DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p
