Index GFF - Revision history

Thomas: Redirected page to Preparing annotation

2013-10-18T15:04:41Z

Redirected page to Preparing annotation

Thomas at 14:10, 6 September 2013

2013-09-06T14:10:04Z

Thomas at 14:06, 6 September 2013

2013-09-06T14:06:09Z

Thomas at 13:54, 6 September 2013

2013-09-06T13:54:41Z

Thomas at 13:53, 6 September 2013

2013-09-06T13:53:45Z

Thomas at 13:53, 6 September 2013

2013-09-06T13:53:12Z

Thomas at 13:53, 6 September 2013

2013-09-06T13:53:05Z

Thomas at 13:52, 6 September 2013

2013-09-06T13:52:33Z

Thomas at 13:52, 6 September 2013

2013-09-06T13:52:05Z

Thomas: Created page with "http://genomeview.org/content/preparing-feature-files"

2013-09-03T20:26:42Z

Created page with "http://genomeview.org/content/preparing-feature-files"

New page

http://genomeview.org/content/preparing-feature-files

← Older revision		Revision as of 15:04, 18 October 2013
Line 1:		Line 1:
−	~~Large feature files need to be indexed before you can use them properly in GenomeView.~~	+	#REDIRECT[[Preparing annotation]]
−
−	~~The definition of large is not strict in the sense that it depends on both the real size of the file, as well as the number of features in the file.~~
−
−	~~<strong>Recommendations:</strong>~~
−	~~<ul>~~
−	~~<li>Only index feature files that are larger than 5 Mb or even 10 Mb when compressed with GZIP.</li>~~
−	~~<li>Only index feature files that do NOT contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. </li>~~
−	~~<li>Typically the~~ annotation ~~of a genome does not need to be indexed if it just contains genes, mRNA, CDS and exons</li>~~
−	<li>You should not included multiple types (mRNA,CDS, ...) of annotation in a single file as all features will be loaded in a single track with the file name as label. We suggest you put each type in its own file.</li>
−	~~</ul>~~
−
−	~~<strong>Instructions:</strong>~~
−	~~To index a file, you need to pre-process it with tabix, much like is done with pile-up files.~~
−
−	~~Tabix can be downloaded from the [https://sourceforge.net/projects/samtools/files/tabix/ tabix download page~~].
−
−	~~== BED formatted files ==~~
−
−	~~sort -k1,1 -k2,2n input.bed \| bgzip -c > compressed.bed.bgz~~
−	~~tabix -p bed compressed.bed.bgz~~
−
−	~~You will get two new files: (1) a bgz file and (2) a tbi file. Load the bgz file in GenomeView.~~
−
−	~~<em>Note that indexing will not work with BED files that have a UCSC header ("track name=blah")</em>~~
−
−	~~== GFF formatted file ==~~
−
−	~~<b>Warning!: Compound features will be broken up during indexing of gff files.</b>~~
−
−	~~sort -T /group/tmp -k1,1 -k4,4n input.gff \| bgzip -c > compressed.gff.bgz~~
−	~~tabix -p gff compressed.gff.bgz~~
−
−
−	~~You will get two new files: (1) a bgz file and (2) a tbi file. Load the bgz file in GenomeView.~~
−
−	~~<em>Note that the structure of genes and the type of annotation features will be lost when indexing gff files.</em>~~

@@ Line 6: / Line 6: @@
 <ul>
 <li>Only index feature files that are larger than 5 Mb or even 10 Mb when compressed with GZIP.</li>
-<li>Only index feature files that do contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. </li>
+<li>Only index feature files that do NOT contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. </li>
 <li>Typically the annotation of a genome does not need to be indexed if it just contains genes, mRNA, CDS and exons</li>
 <li>You should not included multiple types (mRNA,CDS, ...) of annotation in a single file as all features will be loaded in a single track with the file name as label. We suggest you put each type in its own file.</li>

@@ Line 6: / Line 6: @@
 <ul>
 <li>Only index feature files that are larger than 5 Mb or even 10 Mb when compressed with GZIP.</li>
-<li>Only index feature files that do contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. <b>Compound features will be broken up during indexing.</b></li>
+<li>Only index feature files that do contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. </li>
 <li>Typically the annotation of a genome does not need to be indexed if it just contains genes, mRNA, CDS and exons</li>
 <li>You should not included multiple types (mRNA,CDS, ...) of annotation in a single file as all features will be loaded in a single track with the file name as label. We suggest you put each type in its own file.</li>
@@ Line 26: / Line 26: @@
 == GFF formatted file ==
   sort -T /group/tmp -k1,1 -k4,4n input.gff | bgzip -c > compressed.gff.bgz

@@ Line 18: / Line 18: @@
 == BED formatted files ==
-  sort -k1,1 -k2,2n input.bed | bgzip -c > compressed.bed.gz
+  sort -k1,1 -k2,2n input.bed | bgzip -c > compressed.bed.bgz
-  tabix -p bed compressed.bed.gz
+  tabix -p bed compressed.bed.bgz
 <em>Note that indexing will not work with BED files that have a UCSC header ("track name=blah")</em>
@@ Line 26: / Line 27: @@
 == GFF formatted file ==
-  sort -T /group/tmp -k1,1 -k4,4n input.gff | bgzip -c > compressed.gff.gz
+  sort -T /group/tmp -k1,1 -k4,4n input.gff | bgzip -c > compressed.gff.bgz
-  tabix -p gff compressed.gff.gz
+  tabix -p gff compressed.gff.bgz
-In both cases, you will get two new files: (1) a gz file and  (2) a tbi file.
+You will get two new files: (1) a bgz file and  (2) a tbi file. Load the bgz file in GenomeView.
-<strong>Caveat: The structure of genes and the type of annotation features will be lost when indexing gff files.</strong>
+<em>Note that the structure of genes and the type of annotation features will be lost when indexing gff files.</em>

@@ Line 16: / Line 16: @@
 Tabix can be downloaded from the [https://sourceforge.net/projects/samtools/files/tabix/ tabix download page].
-For BED formatted files:
+== BED formatted files ==
   sort -k1,1 -k2,2n input.bed | bgzip -c > compressed.bed.gz
@@ Line 24: / Line 24: @@
 <em>Note that indexing will not work with BED files that have a UCSC header ("track name=blah")</em>
-For GFF formatted files:
+== GFF formatted file ==
   sort -T /group/tmp -k1,1 -k4,4n input.gff | bgzip -c > compressed.gff.gz
@@ Line 33: / Line 33: @@
 Load the gz file in GenomeView.
-<strong>Caveat:</strong>
+<strong>Caveat: The structure of genes and the type of annotation features will be lost when indexing gff files.</strong>

@@ Line 14: / Line 14: @@
 To index a file, you need to pre-process it with tabix, much like is done with pile-up files.
-Tabix can be downloaded from the "[https://sourceforge.net/projects/samtools/files/tabix/ tabix download page].
+Tabix can be downloaded from the [https://sourceforge.net/projects/samtools/files/tabix/ tabix download page].
 For BED formatted files:

← Older revision		Revision as of 13:52, 6 September 2013
Line 1:		Line 1:
−	~~http~~://~~genomeview~~.~~org~~/~~content~~/~~preparing~~-~~feature~~-files	+	Large feature files need to be indexed before you can use them properly in GenomeView.
		+
		+	The definition of large is not strict in the sense that it depends on both the real size of the file, as well as the number of features in the file.
		+
		+	<strong>Recommendations:</strong>
		+	<ul>
		+	<li>Only index feature files that are larger than 5 Mb or even 10 Mb when compressed with GZIP.</li>
		+	<li>Only index feature files that do contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes. <b>Compound features will be broken up during indexing.</b></li>
		+	<li>Typically the annotation of a genome does not need to be indexed if it just contains genes, mRNA, CDS and exons</li>
		+	<li>You should not included multiple types (mRNA,CDS, ...) of annotation in a single file as all features will be loaded in a single track with the file name as label. We suggest you put each type in its own file.</li>
		+	</ul>
		+
		+	<strong>Instructions:</strong>
		+	To index a file, you need to pre-process it with tabix, much like is done with pile-up files.
		+
		+	Tabix can be downloaded from the <a href="https://sourceforge.net/projects/samtools/files/tabix/">tabix download page</a>.
		+
		+	For BED formatted files:
		+	<code>
		+	sort -k1,1 -k2,2n input.bed \| bgzip -c > compressed.bed.gz
		+	tabix -p bed compressed.bed.gz
		+	</code>
		+
		+	<em>Note that indexing will not work with BED files that have a UCSC header ("track name=blah")</em>
		+
		+	For GFF formatted files:
		+	<code>
		+	sort -T /group/tmp -k1,1 -k4,4n input.gff \| bgzip -c > compressed.gff.gz
		+	tabix -p gff compressed.gff.gz
		+	</code>
		+
		+	In both cases, you will get two new files: (1) a gz file and (2) a tbi file.
		+	Load the gz file in GenomeView.
		+
		+	<strong>Caveat:</strong>
		+	The structure of genes and the type of annotation features will be lost when indexing gff files.