Fragment length doesn't change the read generation behaviour

[pabviana]

Hi,

I've noticed that you included the arguments 'fragment length' and 'fragment sd'. I've been trying to use these to specify the read length of the generated reads for a metagenome, but it keeps defaulting to the error model read length.

Could you clarify how these arguments are supposed to work?

Additionally, I noticed that the 'number of reads' argument does not seem to work properly when using the precomputed models. For instance, I tried -n 1m -m miseq, but the generated files only contained 500,000 reads.

Thank you for your assistance.

Best regards,

[ThijsMaas]

Hi,

The read length cannot be changed, as this is a property of the error model and sequencing machine from which it was generated. The fragment length in paired-end sequencing is the total length of both reads including the insert size, allowing you to change this insert size only.

Are you sure the model generated 0.5M reads or 0.5M read pairs, because 0.5M read pairs would be a total of 1M reads. If you need 1M read pairs, you may need to double the number of reads argument.