what are the exact parameters of the presets

[estolle]

Hi there

I am using ngmlr with some raw nanopore reads and its working fine with "--presets ont", However, my average readlength and coverage is not too great, so I was exploring changes to some parameters outlined in the --help. If I use these parameters plus the preset, it appears to not map anything (0 reads mapped). My command was: ngmlr -r $REF -q amc.clone2.pass.porechop.fq.gz -o amc.clone2.pass.porechop2.sam --presets ont --min-residues 200 --threads $CPUs --max-segments 2 The previous command (working) was ngmlr -r $REF -q amc.clone2.pass.porechop.fq.gz -o amc.clone2.pass.porechop2.sam --presets ont --threads $CPUs

THus my Q what the presets for "ont" are, so that I can see if changing them does anything.

Thanks

Eckart

[fritzsedlazeck]

Hi Eckart, This is always tricky to say without looking at some reads. First of all, what is the mean length of your reads? What organism? Are you mapping to an assembly or well established reference? Is it a wgs or an amplicon?

Thanks Fritz

[estolle]

The organism is the honeybee (Apis mellifera, 230 Mb genome, 2 versions I compare to: one older scaffold assembly which is not too bad over all, and since few weeks a "finished" assembly, for both SVs were not called before, its rather a non model organisms for that regard)

reads are 1D ONT, adaptertrimmed with porechop. Fairly short reads. From genomic DNA Bases= 5,836,823,564 contigs= 2481636 mean_length= 2352 longest= 104006 N50= 4532 (n= 328848)

Does the preset change from dataset to dataset?

[fritzsedlazeck]

No it does not. I am just wondering if the min_residue is the one problem maker. We did had problems with that parameter once... So maybe it is worth to try that out. thanks Fritz