Difference between revisions of "Preparing reference sequence"
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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. | 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 [[ | + | 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 | 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. | 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 | + | You can [http://samtools.sourceforge.net download the samtools package from Sourceforge]. |
Latest revision as of 20:01, 18 November 2013
To be able to easily handle large reference genomes, it is required that they are indexed. This can be done with the faidx 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 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.