Snippets

Peter Sudmant managing genome annotations and references

Updated by Peter Sudmant
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File genome_annots Modified

  • Ignore whitespace
  • Hide word diff 
-###annotations and in some cases fasta files for genomes
-
+##############################################
+##annotations and in some cases genome fastas
+##############################################
 /genomes
   /ucsc
     /ucsc
             /{ucsc_version}.gtf
             /{ucsc_version}.gff
       /gtf.index
-
-
-####indexes, based on annotation
-####though, not gtf index for all the
+##############################################
+##indexes, based on annotation (note, not GTFs
+##############################################
 /indexes
   /ucsc
   /ensembl
Updated by Peter Sudmant
View revision

File genome_annots Modified

  • Ignore whitespace
  • Hide word diff 
 ###annotations and in some cases fasta files for genomes
 
 /genomes
+  /ucsc
     /ucsc
-        /ucsc
-            /{species}
-                /{release}
-                    /database/
-                    /fasta
-                        /{release}.fa
-                        /{release}.fa.fai
-                        /ENSEMBL_to_UCSC.contigs
-                        /UCSC_to_ENSEMBL.contigs
-                    /liftover
-                    /phyloP60way
-                    /...
-    /ensembl
+      /{species}
         /{release}
-            /gtf
-                /{species}
-                    /{species_ensembl_version}.gtf.gz
-                    /UCSC
-                        /{ucsc_version}.gtf
-                        /{ucsc_version}.gff
-            /gtf.index
-            
+          /database/
+          /fasta
+            /{release}.fa
+            /{release}.fa.fai
+            /ENSEMBL_to_UCSC.contigs
+            /UCSC_to_ENSEMBL.contigs
+          /liftover
+          /phyloP60way
+          /...
+  /ensembl
+    /{release}
+      /gtf
+        /{species}
+          /{species_ensembl_version}.gtf.gz
+          /UCSC
+            /{ucsc_version}.gtf
+            /{ucsc_version}.gff
+      /gtf.index
 
-####indexes, based on annotation 
+
+####indexes, based on annotation
 ####though, not gtf index for all the
 /indexes
-    /ucsc
-    /ensembl
+  /ucsc
+  /ensembl
+
Created by Peter Sudmant
View revision

File genome_annots Added

  • Ignore whitespace
  • Hide word diff 
+###annotations and in some cases fasta files for genomes
+
+/genomes
+    /ucsc
+        /ucsc
+            /{species}
+                /{release}
+                    /database/
+                    /fasta
+                        /{release}.fa
+                        /{release}.fa.fai
+                        /ENSEMBL_to_UCSC.contigs
+                        /UCSC_to_ENSEMBL.contigs
+                    /liftover
+                    /phyloP60way
+                    /...
+    /ensembl
+        /{release}
+            /gtf
+                /{species}
+                    /{species_ensembl_version}.gtf.gz
+                    /UCSC
+                        /{ucsc_version}.gtf
+                        /{ucsc_version}.gff
+            /gtf.index
+            
+
+####indexes, based on annotation 
+####though, not gtf index for all the
+/indexes
+    /ucsc
+    /ensembl
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