multi fasta input

[alstonius]

Hi,
I'm trying out DeepSimulator on a Bacterial genome where the input fasta has 3 sequences ( chromosome, plasmid_1, plasmid_2). What parameters do I need to set to get, say, 250 simulated reads from this multi-fasta input?

If I simulate 250 reads (-n 250) I obtain 750 reads (i.e. 250 reads per input 'chunk'). I tried setting '-D 0' to concatenate the 3 input chunks but still see 750 reads. The chromosome is the biggest chunk of the genome so I would hope that most of the reads simulated would be derived from the chromosome and not split evenly across the 3 genome features. I must be missing something...

thanks!
Mark

[Markusjsommer]

Same issue here. Need to filter out reads from plasmids etc, otherwise it's very biased

[tim488]

Same here. @liyu95 do you have a recommendation, it's kinda tedious...