Result Formats
Routine Sequencing (rapid turnaround)
Project Sequencing (high throughput)
Routine Sequencing
AB3730xl Platform
Files provided
For each sample, the following files are provided to you:
- sample.ab1: The raw chromatogram trace file. Please refer to the Sequencing troubleshooting guide for further information
- sample.seq: A text file of the sequence, as generated by the sequencing machines
- sample.fa: A FASTA formatted text file containing the high quality clipped sequence
- sample.bn: A text file containing the blastn output for sample.fa against GenBank
Base Calling
The FASTA files in your results are base called from the chromatogram by the KB basecaller from Applied Biosystems. The KB basecaller assesses the quality of each basecall and assigns assigns Phred-like values to each basecall. Please see the AB Fact Sheet for more information regarding the KB basecaller.
Quality Clipping
The .seq file is the text file output from the sequencing machines and contains the basecalls generated from the trace (.ab1) file. There is no assessment of the quality of the base call from the underlying sequence and good and bad quality bases are not discriminated. Therefore the sequence may contain inaccuracies, particularly towards the ends of the sequence. In addition, if the sequencing reaction has failed, a .seq file will still be produced even though the trace quality is very poor. If the poor quality portions of the sequence read are included in a BLAST analysis, this may give misleading results.
A shorter, but higher quality, sequence is contained in the .fa file, which has been extracted from the chromatogram via quality clipping. The FASTA file has been generated by using a sliding window over the length of the chromatogram, once the quality falls below the threshold within this window, a clip is introduced, thus removing the poor quality bases from the ends. Quality values are assigned using the KB Base caller. Please see the AB Fact Sheet for more information regarding the KB basecaller.
Blast Results
The quality clipped sequence (given in the sample.fa file) is blasted against the latest release of the GenBank database using blastn. The results are then recorded in the .bn file. The top 30 hits from the blastn search are recorded. For more information about BLAST click here
Quality Failed Sequences
In the event that quality clipping did not yield a product of at least 11bp of good quality sequence (11bp being the cutoff search size of a typical blastn query) the .fa and .bn files will be generated as follows:
sample.fa
>sample
Sequence too short to blast (<11bp) after quality clipping
sample.bn
sample
Sequence too short to blast (<11bp) after quality clipping
Project Sequencing
Files provided
For each sample, the following files are provided to you:
- sample.ace: ACE format assembly file for viewing in an assembly viewer e.g. consed
- sample.fna: A multi FASTA format file of all Contigs >500 nucleotides
- sample.qual: A multi FASTA format file of the quality file which corresponds to the .fna file
Many other types of analysis may be provided on request. Please contact us for further information.
Files provided
For each sample, the following files are provided to you:
- sample.ace: ACE format assembly file for viewing in an assembly viewer e.g. consed
- sample.LargeContigs.fna: A multi FASTA format file of all Contigs >500 nucleotides
- sample.LargeContigs.qual: A multi FASTA format file of the quality file which corresponds to the .fna file
- sample.AllContigs.fna: A multi FASTA format file of all Contigs
- sample.AllContigs.qual: A multi FASTA format file of the quality file which corresponds to the .fna file
Many other types of analysis may be provided on request. Please contact us for further information.
Microarrays
Clients are provided with Excel spreadsheets for microarray results as follows:
- Normalised values of all the probes/genes across all the chips
- Differentially expressed genes along with Fold-change and/or P-values, and annotations
- Molecular Function Statistics of differentially expressed genes
- Cellular Component Statistics of differentially expressed genes
- Biological Process Statistics of differentially expressed genes
