nanopolish
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jts
Signal-level algorithms for MinION data
python3 /home/niabguest/krishna/apps/nanopolish/scripts/nanopolish_makerange.py /home/niabguest/krishna/hyl2_basecalling/canu_assembly/trim_assembly/assembly_small/assembly.contigs.fasta | parallel --results /home/niabguest/krishna/apps/nanopolish/scripts/nanopolish.results -P 7 /home/niabguest/krishna/apps/nanopolish/nanopolish variants --consensus -o /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/polish.{1}.vcf -w {1} -r /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/1D_mapping/basecall.fastq.gz -b /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/mapping/samindex_mapping.sorted.bam.bai -g /home/niabguest/krishna/hyl2_basecalling/canu_assembly/trim_assembly/assembly_small/assembly.contigs.fasta t-14 I'm using the above command for polishing...
Hi nanopolish team! I wonder if there are any settings to prevent skip as showed below when using nanopolish eventalign? As you know, eventalign assigns events to bases accoding to...
Hi Jared, As requested I open a new issues due to the discrepancy between the "read count" output from nanopolish index and eventalign commands. Here is an example from one...
I have 1000X raw data of nanopore reads, and I have called the methylation of genome according to "https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html", and I have got the result with low methylated_frequency. Should I...
Hello, thanks for this awesome tool. I have a question about the samples for one event. Are they dependent or independent? I mean one signal measurement for event1 could affect...
Hi,i have some problem when i run nanopolish call-mythlation for GM12878. The indexing is normal, but in call-mythlation i met this issue: ``` nanopolish-0.14.0/nanopolish call-methylation -b GM12878/chr1/GM12878.sort.bam -g human_ref/GRCh38.p13.genome.fa -r...
`htslib` build fails without `bzip2` libraries. Added `bzip2-devel` yum package to Dockerfile.
Hi there, I am trying to install nanopolish as a dependency for another tool, EpiNano. I am running this on a computing cluster and was able to clone the github...
Hi there, I am running nano polish with this command: python3 nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 20 \ nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r reads.fa -b...
Hi there, Would it be possible to udpate the version of nanopolish working in conda please ? Best, Elodie
