jagos01

I am having the same issue. I have tried the standard and alternative methods of installation and both fail with an error in rule map_minimap2 [2019-08-27T130612.565348.snakemake.log](https://github.com/nanoporetech/pipeline-structural-variation/files/3551263/2019-08-27T130612.565348.snakemake.log)

Hello Zhuofei, I error corrected the Ion Torrent data using spades (--iontorrrent and --only-error-correction flags) and then converted the fasta file to fastq with the attached script (use script at...

Hello Zhuofei, Sorry for the late reply. Here is a link to the script I used for the conversion (fasta_to_fastq.pl). https://code.google.com/archive/p/fasta-to-fastq/ Scott

Hello mradz19, I only used spades to correct the ion torrent data. I then did a hybrid assembly with unicycler using spades corrected ion torrent reads and raw nanopore reads.

Thanks for your quick reply. I will try it out when it is released.

Hello @onordesjo, I followed the directions outlined in the readme for duplex calling with dorado. I generated the pair_id files for both step 2a and 2b. They contained 4667 and...

Hello @onordesjo. This is bacterial whole genome sequence data. No amplification was carried out. The data is split over two runs (had to restart the sequencer a couple hours into...

I inspected the pod5 reads for each run and the unmapped BAM file contains reads from both runs.

Thanks, I have emailed a link to the bam file.