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I have been trying to assemble a 10Mb genome with uncorrected nanopore data (3-4 chromosomes expected). We have a lot of data, is that the reason Flye fails at the end?
[2019-06-22 11:00:05] INFO: …
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I just tried to assembly the tetraploid with MaSuRca 3.2.7, but the file "PLOIDY.txt" shows "1", how can I fix that?
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Greetings,
I've been using gatb-minima-pipeline for a while now for a de novo assembly software benchmark, available at [Github](https://github.com/cimendes/LMAS). I've been running it so far witho…
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## methylation distribution on read
I want to analyze the RNA m6A modification. I selected m6A_DRACH model when dorado basecaller.
Then I use modkit for downstream analysis.
`modkit pileup $bam \
…
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### Background
Randstrobes is a method for linking two or more k-mers together into a seed that can be used for sequence mapping. I intend the below post to be a self-contained rough description of…
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I would like to adjust the repeat time for analyzing the reads. In 'deep simulator 1.0' paper as attached in the pdf, there is a parameter in page number 7 called 'a' for adjusting. But I couldn't fin…
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Hi there,
I am trying to simulate nanopore amplicon reads (~6.5 kbp longest amplicon, ~37 kb total sequence) but the simulation part seems to hang and never proceed. I was able to train an error pr…
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Hi Jennifer,
My apologies in advance if there is an solution already.
I'm using bracken together with the pre-built silva 138 db.
Command is:
```
bracken \
-d /home/Staff/uqgni1/tools/kraken2…
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I have been facing several issues while running the snpArcher pipeline on a SLURM cluster,
Incomplete Files and --rerun-incomplete Flag: Initially, I encountered incomplete output files being gener…
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Hi,
I've been puzzled by the lack of calls/site for CHG and CHH methylation for a few days now. I called similar data with Megalodon and modbamtobed a year or two ago and got very different results…