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shendurelab / MIPGEN

One stop MIP design and analysis
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Ext_Probe_copy & lig_probe_copy #55

Open Kapilavasthi6 opened 1 month ago

Kapilavasthi6 commented 1 month ago

I am ruining MIPGEN with very basic options, but in my output ....picked_mips.txt file does not contain any number in Ext_Probe_copy & lig_probe_copy getting only 0. (../MIPGEN/mipgen -regions_to_scan practice_genes.bed -project_name practice_design -min_capture_size 162 -max_capture_size 162 -bwa_genome_index //human_g1k_v37.fa)

augustboyle commented 3 weeks ago

Are you sure you're using the right path for your bwa_genome_index? The example should still be able to run.

Kapilavasthi6 commented 3 weeks ago

Yes, I downloaded the same file from the UCSC (human_g1k_v37.fa), used with the (mipgen -regions_to_scan Practice_genes.bed -project_name Practice_genes -min_capture_size 38 -max_capture_size 60 -max_mip_overlap 0 -max_arm_copy_product 10 -bwa_genome_index human_g1k_v37.fa