Preparing reference sequence - Revision history

69.173.108.246 at 18:01, 18 November 2013

2013-11-18T18:01:39Z

2013-11-18T18:00:59Z

2013-10-17T23:21:36Z

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

New page

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

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 To be able to easily handle large reference genomes, it is required that they are indexed. This can be done with the <em>faidx</em> command from the samtools package.
-If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the [[BAM|short read preparation page]] or you can skip the step there whenever you're ready.
+If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the [[Preparing_read_data|short read preparation page]] or you can skip the step there whenever you're ready.
 To index a fasta file you run
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 If your file was called reference.fasta, GenomeView will search for reference.fasta.fai in the same directory. If you want to be able to load large files, make sure those two files are correctly named and in the same folder.
-You can <a href="http://samtools.sourceforge.net/">download the samtools package from Sourceforge</a>.
+You can [http://samtools.sourceforge.net download the samtools package from Sourceforge].

← Older revision		Revision as of 18:00, 18 November 2013
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−	http://~~genomeview~~.~~org~~/~~content~~/~~preparing-fasta-files~~	+	To be able to easily handle large reference genomes, it is required that they are indexed. This can be done with the <em>faidx</em> command from the samtools package.
		+
		+	If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the [[BAM\|short read preparation page]] or you can skip the step there whenever you're ready.
		+
		+	To index a fasta file you run
		+	samtools faidx reference.fasta
		+
		+
		+	==Attention==
		+	If your file was called reference.fasta, GenomeView will search for reference.fasta.fai in the same directory. If you want to be able to load large files, make sure those two files are correctly named and in the same folder.
		+
		+	You can <a href="http://samtools.sourceforge.net/">download the samtools package from Sourceforge</a>.