nanopolish
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jts
Signal-level algorithms for MinION data
I am running nanopolish variant calling on chr22 of a NA12878 dataset. I generated small regions using the *make range script* and launched multiple nanopolish instances using *parallel* command. However,...
Travis CI announced 2 days ago that travis-ci.org shut down will occur on May 31, 2021. https://blog.travis-ci.com/2021-05-07-orgshutdown We need to migrate travis-ci.org to travis-ci.com, otherwise maybe we can not continue...
Hello, I'm running nanopolish index and eventalign on a puc19 dataset downloaded on SRA with the accession SRR5219626. I have downloaded the fast5 files and I used a fast5 to...
Adds 95% confidence intervals to read rate and poly(A) length estimates by performing bootstrapped resampling of kmer durations. By default this is switched off and the output should be identical...
Running nanopolish eventalign on direct RNA data, basecalled with guppy 3.6.1 with parameters `--samples --print-read-names --scale-events` fails with the error `nanopolish: src/nanopolish_squiggle_read.cpp:1107: std::vector SquiggleRead::get_scaled_samples_for_event(size_t, size_t) const: Assertion `curr_sample_time >= (this->sample_start_time...
I helped a colleague debug an issue with nanopolish call-methylation, whereby a BAM file with no spliced alignments would be detected as having a spliced alignments, leading to the program...
Hello I called the methylation on your example data and I ran the calculate_methylation_frequency.py tools to get the methylation_frequency.tsv file. Now I would like to launch compare_methylation.py using the bisulfite.ENCFF835NTC.example.tsv...
I've been trying to call somatic variants in a diploid organism, and so would like to set `--ploidy 4` for `nanopolish variants`. Whenever I do this, however, I get the...
Hi, Is it possible to speedup eventalign computations by splitting the files and/or region windowing? For example to speedup `nanopolish eventalign --reads all.fastq --bam all.bam --genome genome.fa > all.tsv`, split...
Hello, Please kindly have a look. I presume that the time fixing this pay off easily when there are error reports. :o) Steffen ``` g++ -o src/nanopolish_call_variants.o -c -g -O2...
