See our User Agreement and Privacy Policy. See our Privacy Policy and User Agreement for details. Create your free account to read unlimited documents. The SlideShare family just got bigger. Home Explore Login Signup. Successfully reported this slideshow. We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Next SlideShares. You are reading a preview. Create your free account to continue reading. Sign Up. Upcoming SlideShare. Embed Size px. Start on. Show related SlideShares at end. WordPress Shortcode. Share Email. Top clipped slide. Download Now Download Download to read offline. The file is plain text and thus can be read with a text editor. Genbank files often have the file extension '. The format is used by sequencing facilities and require special readers capable of reading the file format to view the trace data and extract the sequence.
The file format is difficult to parse given its binary nature and the complexity of the spec. PDB - the PDB file format is used to store both sequence information, but more importantly stores 3-dimensional structure information. This information can be used to visualize the crystal structure of a given molecule typically a protein. Where each instance of Identifier, Bases, and Qualities are newline-separated.
Although generally the case, there are some instances where paired reads are not a forward read paired with a reverse read. Under Roche , SRA accepts both 'pre-split' or 'post-split' fastq sequences. Paired 'post-split' reads must be provided in separate files or in the interleaved format. The native format for helicos is fasta so converting to fastq requires creating a default quality score.
The default value selected by the SRA team is '14'. Fasta files adhering to the definition lines described in the fastq section are acceptable, too, although fastq is preferred a file type of fastq should still be specified.
The SRA assigns a default quality value of 30 in this case and expects this format:. Fasta files may be submitted with corresponding qual files, too. These are recognized in the SRA data processing pipeline as equivalent to fastq and should be specified as fastq when submitting the data files. Files from some platforms mostly older Illumina and Roche employing this format are acceptable and the entries in the pair of files should look like:.
In a given pair of files, there must be the same number of reads in both. These formats are still accepted by SRA, but are considered out-of-date and not recommended for submission. If you are able to update your files to a more common format please do so before submitting to SRA. This format has sufficient flexibility to store data from current and future DNA sequencing technologies. This is a single input file format for all downstream applications and a read lookup index enabling downstream formats to reference reads without duplication of all of the read specific information.
Within a related set of files, reads are grouped by tile. Reads should be fixed length, and the number of quality scores and bases is the same in each.
0コメント