Is it possible to control number of reads that are simulated?

[zuegereliane]

I am wondering how the total number of simulated reads that BEERS2 outputs are determined (i.e the equivalent to sequencing depth in a real experiment). Looking through the documentation I and config files I have not found anything. Is there a parameter to specify this?

[tgbrooks]

Hi, there is no way to select ahead of time the exact number of reads to be created. Instead, BEERS2 generates reads based off the input sample give: to get more reads out, increase the input sample. Try increasing num_packets and num_molecules_per_packet if using the from_distribution_data input option or increasing the number of molecules in your input if using the molecule file input option.

I recommend running the pipeline with a small number of input molecules, seeing how many output molecules you get, and then scaling up the input to achieve the desired number of output molecules.

The number of reads generated is also influenced by many other parameters. For example, fragmentation parameters and size selection parameters will alter how many molecules are available for later parts of the sequencing pipeline. Of course, these parameters also affect the size of the sequenced fragments. The retention_percentage is also a major determinant of how many molecules are retained after PCR and hence sequenced: however, altering this parameter also affects the PCR dupe rate. Therefore, I typically do not alter these parameters unless they are what we're assessing.