Commit 4cdc54b5 authored by Tizian Schulz's avatar Tizian Schulz
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Update README.md

parent ba89dc3b
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Alignment results are outputted on the command line seperately for each query. They reveal a perfect match for each query and various suboptimal ones.
Repeating the search a second time using parameter `-r` allows us to get information about the individual samples from the graph involved in each alignment. Both perfect matches (first result for each query) are completely covered by a sample of Marburg virus and partially by a second sample (*NC_001608v3*) as well.
Repeating the search a second time using parameter `-r` allows us to get information about the individual samples from the graph involved in each alignment. Both perfect matches (first result for each query) are completely covered by a sample of Marburg virus (*NC_024781v1*) and partially by a second sample (*NC_001608v3*) as well.
Assuming we are particularly interested in how alignments look for NC_001608v3, we could specify a *search set* for our search. It allows to focus alignment searches inside the graph exclusively to sequences from certain samples. A search set may be passed to the algorithm using a text file with one *sample id* per line. A sample id here means the sample's file path used for graph building.
A search set for our current use case may be found below the *testdata* directory, too.
......@@ -185,7 +185,7 @@ PLAST [COMMAND] [COMMAND_PARAMETERS]
PLAST Search -i ebolaPangenome -q unknownQueries.q -w 12 -Q 80
```
allows to find all alignments supported by at least 50% of all samples of our Ebola graph.
allows to find all alignments supported by at least 80 (50%) of all samples of our Ebola graph.
4. **Alignment statistic parameter estimation**
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