Ognjen Milicevic

Missed variant at 241, outputted by minimap2 https://ibb.co/Js8F18t

Thanks for a prompt reply. Can you help me check that? Do I use samtools on BAM for that, or is it something that is done on FASTQ like average...

I guess this is pertinent for your question: https://ibb.co/pnrkS4v Also, for the sequencing run speed over time: https://ibb.co/wNpdQQ8 Please, teach me how to fish :)

Ah, pardon. Here it is: https://ibb.co/s2qpQJx If this is all ok, what could cause the rejection of so many reads? And then, is it expected that the remaining reads cannot...

After MinKnow, I used [Artic](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html) pipeline command: artic guppyplex --min-length 400 --max-length 700 --directory output_directory/barcode03 --prefix run_name Fail VCF is also empty. If it helps, I am willing to share...

Here are the files: https://medbgacrs-my.sharepoint.com/:f:/g/personal/ognjen_milicevic_med_bg_ac_rs1/EpcF8O67m5RMn19T01rgqXcBuh3M4frWZvp2y6I6w3B9Jw?e=aBD6AC It will take some hour more for fast5 upload to finish. Thanks, I am not in a hurry for results, but it would be cool...

Thank you for your effort. Nanopolish 0.13.2 Guppy 4.2.2+effbaf8

$GUPPY -i $FOLD/$BC -s $OUTPUT --flowcell FLO-MIN111 --kit SQK-LSK109 --device $GPU artic guppyplex --min-length 400 --max-length 700 --directory $OUTPUT --prefix $OUTPUT/filtered

First of all, thank you for this great insight. I would impose on your knowledge for a bit more. 1. We would gladly test this with the r10 branch, but...

Thank you for a prompt reply. Would you say that with more than 10 samples the classical method would give robust estimates, and there is no need for empirical distributions?...