Comments (4)
Do you have a sample fast5
file you can send through so we can test and fix?
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Hmm it seems nanopore has made it quite complicated. First the reads are all 1D basecalled and a FAST5 is made. When the basecalling is finished, there is the possibility to run another script which looks which reads are 1Dsquared and writes the results immediately to a FASTQ file. So I guess it isn't possible to run npreader on this.
from japsa.
Without sample data we are unable to test if we can get it working. Are you able to point us in the direction of some 1D-squared data we can test on? I can't seem to find any.
from japsa.
no answer
from japsa.
Related Issues (20)
- BC01 empty HOT 1
- Resistance profiling Exception in thread "SSS" java.lang.NullPointerException HOT 1
- Release v1.7-05b - jsa.np.npreader HOT 1
- Feature request - use floats for base-call quality averages for jsa.np.filter params HOT 3
- problem with A dynamic, reusable donut chart for D3.js v4 HOT 4
- option illen doesn't work in capsim HOT 2
- Duplicated reads id issue HOT 1
- Refactor `consensusSequence()` HOT 2
- Species binning of fastq HOT 1
- VNTRTyper ArrayIndexOutOfBoundsException when handling BAM records with >65535 CIGAR operations HOT 2
- XM data corruption
- VNTR.xaf HOT 4
- Installation failed HOT 3
- identity rate in jsa.hts.errorAnalysis
- Understanding of jsa.np.rtSpeciesTyping output HOT 2
- NullPointerException XM compression HOT 2
- java.lang.OutOfMemoryError: Requested array size exceeds VM limit
- jsa.np.rtResistGenes - tmp folder not automatically generated, and _ao.fasta not produced when tmp folder made in advance HOT 1
- introducing new variable starting with word 'read' triggers ambiguity in japsa.util.CommandLine
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