Demultiplexing fastq files. Undocumented Illumina feature.

Question

[BioApps]

I am building a full blown fastq/sff editor: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files

While building the demultiplexing module I ran into a FastQ with strange Illumina encoding. First line (sequence identifier) of each sequence looks like this: @ERR000897.6134690 IL10_747:8:330:47:613/1

This is not a valid Casava 1.8 formatting but also not a Casava 1.0. Could be something in between? Illumina didn't bother to document also the old formats.

Answer 1

[Adrian Pelin]

I believe this is something coming from a SRA file that was converted to fastq with fastq-dump from the SRA Toolkit. The identifier is the run number, you can view it here: http://www.ncbi.nlm.nih.gov/sra/?term=ERR000897

[BioApps]

Then I have to check the SRA documentation to see if it contains demultiplexing info.

Mersi mult.