From 53df98255d7a59fd2c99e74c6f7487a1bd698f3b Mon Sep 17 00:00:00 2001
From: tcarver <tjc@sanger.ac.uk>
Date: Thu, 1 Nov 2012 12:02:03 +0000
Subject: [PATCH] add indexed GFF support
---
docs/file_menu.sgml | 33 ++++++++++++++++++++++++++++-----
1 file changed, 28 insertions(+), 5 deletions(-)
diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index 2a51aba15..64cc961f3 100644
--- a/docs/file_menu.sgml
+++ b/docs/file_menu.sgml
@@ -44,11 +44,34 @@ This function only reads the feature section of the input file - the sequence
</LISTITEM>
<LISTITEM>
<PARA>
- FASTA files and indexed FASTA files can be read. The files are indexed
-using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK> (e.g.
-<COMMAND>samtools faidx ref.fasta</COMMAND>). A drop down menu of the contigs or chromosomes
-is provided in the Entry toolbar to select the sequence. Using indexed FASTA files
-improves the memory management and enables large genomes to be viewed.
+ FASTA files
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+ Indexed FASTA files can be read in. The files are indexed
+using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK>:
+ </PARA>
+ <SYNOPSIS>
+samtools faidx ref.fasta
+ </SYNOPSIS>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+The indexed FASTA can be used with an indexed GFF to overlay annotation on the sequence.
+To index the GFF first sort and bgzip the file and then use tabix with "-p gff" option (see the
+<ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK>):
+ </PARA>
+ <SYNOPSIS>
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
+tabix -p gff sorted.gff.gz
+ </SYNOPSIS>
+ <PARA>
+A drop down menu of the contigs or chromosomes sequences is provided in the Entry toolbar
+to select the sequence. Using indexed FASTA and indexed GFF files improves the memory management
+and enables large genomes to be viewed. Note that as it is indexed the sequence and annotation are
+read-only and cannot be edited. When there are many contigs to select from it can be easier
+to display the one of interest by typing the name into the drop down list.
</PARA>
</LISTITEM>
<LISTITEM>
--
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