Category: "Sequencing"

FASTQ Sequence Files

December 15th, 2010
A good description of the FASTQ format can be found at Illumina: "A fastq file is an ASCII encoded text file that stores DNA or RNA sequences and their corresponding IDs and quality scores. It uses unix newlines and consists of 4 lines per sequence un… more »

RNA-Seq data quality scores

February 26th, 2010
There are different way to encode the quality scores in FASTQ files. It is important to know these before using the data and converting between the ways if necessary. Sanger format can encode a [[Phred quality score]] from 0 to 93 using [[ASCII]… more »

The SRF Format

July 2nd, 2009
SRF (Sequence Read Format) is a generic and flexible container format for sequencing and next-generation sequencing files. Format working group: http://srf.sourceforge.net It's the preferred format for the submission of sequencing results to archives… more »

Next-Gen Sequence-Submissions to the ENA

June 3rd, 2009
New Sequencing results are submitted to the European Read Archive (ERA) - now called European Nucleotide Archive (ENA) which collaborates with the NCBI Short Read Archive (SRA). Documentation (EBI) General guidelines (NCBI) Meta data hierarchy:… more »