FASTQC and csfasta files

[jarthur]

Hello all,

I have some SOLID data (i.e., data_F3.csfasta and data_F3_QV.qual). As I understand, FASTQC should accept colour space data. However, when I open the above files I get:

"File format error: ID line didn't start with '@'"

How do open colourspace data in FASTQC? Thanks.

Regards,

Jonathan

[maubp]

It sounds like it is expecting (colour space) FASTQ, while you have colour space FASTA + QUAL.

Unless it can be told to read FASTA+QUAL, you'll need to convert the pair of files into a FASTQ file first.

[colindaven]

FastQC accepts bam format, so you can run a read alignment and read that in.

I haven't got it working on csfasta + qual files yet, and probably won't try.

NGSQC is supposed to be a platform independent QC program, and is on my list of programs to establish.