add step to combine repeatmodeler repeats with repbase repeats

blaxterlab · Feb 24, 2016 · cf785c7 · cf785c7
1 parent 319a864
commit cf785c7
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diff --git a/docs/combine-repeat-libraries.txt b/docs/combine-repeat-libraries.txt
@@ -0,0 +1,19 @@
+.. _combine-repeat-libraries:
+
+########################
+Combine Repeat Libraries
+########################
+
+Use the :ref:`repeatmasker` tool ``queryRepeatDatabase.pl`` to extract
+taxon-specific repeats:
+
+::
+
+  /exports/software/repeatmasker/repeatmasker-4-0-5/util/queryRepeatDatabase.pl \
+         -species "taxon" > repeatmasker.taxon.fa
+
+and combine with a repeatmodeller library:
+
+::
+
+  cat repeatmasker.taxon.fa taxon.consensi.fa.classified > taxon.repeatlib.fa
diff --git a/docs/repeat-masking.txt b/docs/repeat-masking.txt
@@ -12,4 +12,5 @@ Contents:
    builddatabase
    repeatmodeler
    filter-repeatmodeler-library
+   combine-repeat-libraries
    trf