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Hello,
I am trying to perform an assembly with some pacbio and some nanopore reads and my job stop quite early on without much explanation.
The command I used is:
```
canu \
-p doublon-mix …
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Hi~
I have a question about the fastq files of rel3. As far as I know, after the nanopore minion sequencing, the fastq files and fast5 files will be classified into two directiories including "pass"…
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Hello,
I am trying to assemble a lot of pacbio reads (100x) with a few (5x) minion reads. This is the command I have used. I am running on a cluster via slurm.
#SBATCH --cpus-per-task=8
#SBATCH…
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Consider these examples (mostly tools I am familiar with, picked to show three different licenses):
- https://bioconda.github.io/recipes/khmer/README.html
- License: BSD-3-Clause
- https://bioc…
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Hi,
I am runing canu to assemble lambda genome that I have got from MinIOn. In the gatekeeperPartion step, I got following error:
> Finished on Sun Oct 9 19:09:15 2016 (lickety-split) with 417.045 G…
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Hello,
While the pychopper ran successfully (with conda installation), all the reads from my MinION run was unclassified (from the stats.output) :
+ - unclassified
0 0 2…
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Does anyone have experience with taking the resulting .sam/.bam files from minimap2 and funneling them into a differential analysis package? Specifically, I am looking to take reads from Direct RNA se…
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Hi, I'm a new user of the famous CANU. I wanted to assemble de novo a set of Nanopore gDNA reads (~800Mb) to get closer to a bacterial genome, which size is expected to be close to 4.5Mb.
I ran the f…
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I have previously used phyloseq to help analyse 16s data from illumina processed using QIIME generating biom file and using the ouitput of the core diversity analysis. I now have metagenomic data from…
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Hello,
Hello, I am trying to use Nanopolish v.11.0 on the Flux Linux-based operating environment at the University of Michigan to polish assembled contigs from Canu v1.8 of demultiplexed amplicons …