Long inserts

[Malabady]

Hello,

Is there any limitations on the target insert size? I want to design high density MIPS for small genome with insert length target > 1300. Is this possible? If yes, do you have any recommendations about the parameters that I should adjust?

Thanks,

[augustboyle]

Hello,The training set should enable decent performance up to 250 nt inserts. At your intended size I don’t think the scoring will be very accurate. That said the functionality may still be useful for rolling regions if you are targeting a large number of loci. I would advise using a narrow range of parameters so the probes are more similar to each other and the scoring does not play a large role in selection.EvanCourtesy of my phoneOn Oct 23, 2023, at 12:49 PM, Malabady @.***> wrote: Hello, Is there any limitations on the target insert size? I want to design high density MIPS for small genome with insert length target > 1300. Is this possible? If yes, do you have any recommendations about the parameters that I should adjust? Thanks,

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[Malabady]

Thanks!

what do you think about the following parameters:

./mipgen -regions_to_scan WG.bed \ -project_name SC2-design \ -min_capture_size 1000 \ -max_capture_size 1500 \ -bwa_genome_index genome.fasta \ -capture_increment 1 \ -max_mip_overlap 900 \ -check_copy_number off \ -double_tile_strands_separately on \ -target_arm_copy 30

I am designing for the whole genome, which is only 30Kb genome. So, it is once locus. What would you change in these parameters?

Many thanks,

[augustboyle]

Hello,I thought I would follow up and say that I didn’t see any big issues with those options but of course I couldn’t say whether they will satisfy your use case in the end!Best of luck,EvanCourtesy of my phoneOn Oct 23, 2023, at 6:08 PM, Malabady @.***> wrote: Thanks! what do you think about the following parameters: ./mipgen -regions_to_scan WG.bed
-project_name SC2-design -min_capture_size 1000 -max_capture_size 1500 -bwa_genome_index genome.fasta -capture_increment 1 -max_mip_overlap 900 -check_copy_number off -double_tile_strands_separately on -target_arm_copy 30 I am designing for the whole genome, which is only 30Kb genome. So, it is once locus. What would you change in these parameters? Many thanks,

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