fastq-dump for Illumina

[duygu]

Hi all,

Does anybody know whether it will be kosher to use the default settings of fastq-dump (Q=33) for Illumina datasets ? I am not sure whether the original Illumina reads are generated using the Sanger offset or not. Would it even make a difference to use the default Q setting for converting Illumina sra data into fastq format?

Thank you!
Duygu

[maubp]

If you're using data from the SRA, then the SRA tool should dump out Sanger FASTQ (offset 33).

If your data is direct from an Illumina machine, it depends on the version of the pipeline which type of FASTQ you'll get. The latest version generates Sanger FASTQ.

[duygu]

Hi,

Let me clarify. I am using data from SRA but the original datasets are generated by Illumina. Therefore I am confused whether using Sanger Fastq for Illimuna datasets would make any sense.

Thank you for your help!!

[maubp]

I'm pretty sure they'll be using the Sanger FASTQ standard.