Difference between revisions of "Metagenomics sequence formats"

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(File formats)
(File formats)
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To upload sequence data to the metagenomics RAST server, we accept several file formats.  
 
To upload sequence data to the metagenomics RAST server, we accept several file formats.  
  
* You can upload a fasta file containing ''just the nucleotide sequences''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size.
+
* You can upload a fasta file containing '''just the nucleotide sequences'''. This is the simplest format, just have a regular [[Valid fasta format]] nucleotide sequence file, and upload it. However, there may be some limitation on the file size.
  
* You can compress the sequence file containing ''just the nucleotide sequences'' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up.
+
* You can compress the sequence file containing '''just the nucleotide sequences''' with [http://www.gzip.org/ gzip], a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up.
  
* You can also include a ''separate'' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!):
+
* You can also include a '''separate''' quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!):
  
 
     gzip archive.gz sequence.fa sequence.qual
 
     gzip archive.gz sequence.fa sequence.qual
  
 
If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional.
 
If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional.

Revision as of 07:46, 5 October 2007

File formats

To upload sequence data to the metagenomics RAST server, we accept several file formats.

  • You can upload a fasta file containing just the nucleotide sequences. This is the simplest format, just have a regular Valid fasta format nucleotide sequence file, and upload it. However, there may be some limitation on the file size.
  • You can compress the sequence file containing just the nucleotide sequences with gzip, a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up.
  • You can also include a separate quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!):
   gzip archive.gz sequence.fa sequence.qual

If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional.