User: wangdp123
wangdp123 • 120
- Reputation:
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- Location:
- Oxford
- Last seen:
- 1 day, 9 hours ago
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- 2 years, 7 months ago
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Posts by wangdp123
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... Thanks for this.
I have a quick look at the database but couldn't find the list of genomes that have been included in the database. Am I missing something?
...
written 1 day ago by
wangdp123 • 120
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... To clarify the process, the batch script test.sh looks like this:
> \#Request running time
> \#$ -l h_rt=48:00:00
> \#Request the number of nodes
> \#$ -l nodes=10 (each node has 16 cores, thus in total 160 cores available from 10 nodes)
> \#Request the memory
> \#$ -l h_vmem= ...
written 1 day ago by
wangdp123 • 120
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... Hi there,
I have a long standing unresolved question about the difference between heatmap.2 and pheatmap.
In general, we could see the clusters produced by pheatmap exhibit a more obvious color pattern (the genes with the similar colors in each row will cluster together first) rather than heatmap. ...
written 1 day ago by
wangdp123 • 120
• updated
1 day ago by
Kevin Blighe ♦ 30k
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... What if only put --cores=160 in the snakemake script without using the --cluster argument and then qsub the batch script ?
...
written 1 day ago by
wangdp123 • 120
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... Hi there,
I am thinking about how to use snakemake under the HPC system. Can snakemake work with multiple nodes from HPC?
For example, I request 8 nodes and each node has 20 cores in the batch script and as a result, I totally request 8*20=160 cores.
And then I set the --cores=160.
snakemake --c ...
written 1 day ago by
wangdp123 • 120
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... Hi there,
I am investigating the data from OrthoDB and trying to find out if the data include the orthologs between human and bacteria.
At the first glance, it seems it doesn't have such kind of data. The orthology identification is restricted within each major clade only.
Any suggestions? Am I n ...
written 28 days ago by
wangdp123 • 120
• updated
1 day ago by
Christophe Dessimoz • 480
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... Hello,
Does anyone notice that when running twice cuffdiff software for the same dataset, the resultant q_value could be slightly different (not exactly the same)?
Is this normal? Why could this happen?
Many thanks,
Tom
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... Hi there,
Does anybody know a decent tool that can plot the saturation curve for RNA-Seq data in order to estimate how many reads will be enough to accurately measure the stable gene expression levels?
I tried to search but couldn't get a clear answer.
Thank you very much,
Tom
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... Hi, thanks for this.
I have checked the standard error file, which includes the following message:
*** caught segfault ***
address 0x17a34e074, cause 'memory not mapped'
In addition, the same set of fastq files can be mapped against the genome without problem via Tophat2.
Does this ...
written 8 weeks ago by
wangdp123 • 120
1
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... Hi there,
When running align function in Rsubread package for one particular RNA-Seq samples, an error message "Segmentation fault" came up and the program stopped at "50% completed". It works for other samples but only doesn't work for this sample.
Does anybody know how to tackle this problem?
T ...
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For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
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For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
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For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
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