User: wangdp123

gravatar for wangdp123
wangdp123120
Reputation:
120
Status:
Trusted
Location:
Oxford
Last seen:
1 day, 9 hours ago
Joined:
2 years, 7 months ago
Email:
w********@gmail.com

Posts by wangdp123

<prev • 52 results • page 1 of 6 • next >
0
votes
2
answers
92
views
2
answers
Comment: C: Use OrthoDB to retrieve the orthologs between human and bacteria
... 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 wangdp123120
0
votes
0
answers
108
views
0
answers
Comment: C: Can snakemake work with multiple nodes from HPC?
... 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 wangdp123120
0
votes
1
answer
85
views
1
answer
The difference between heatmap.2 and pheatmap
... 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. ...
rna-seq heatmap written 1 day ago by wangdp123120 • updated 1 day ago by Kevin Blighe30k
0
votes
0
answers
108
views
0
answers
Comment: C: Can snakemake work with multiple nodes from HPC?
... 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 wangdp123120
3
votes
0
answers
108
views
0
answers
Can snakemake work with multiple nodes from HPC?
... 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 ...
hpc snakemake written 1 day ago by wangdp123120
1
vote
2
answers
92
views
2
answers
Use OrthoDB to retrieve the orthologs between human and bacteria
... 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 ...
orthologs orthodb written 28 days ago by wangdp123120 • updated 1 day ago by Christophe Dessimoz480
0
votes
0
answers
104
views
0
answers
q_value in cuffdiff results
... 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 ...
cuffdiff rna-seq written 4 weeks ago by wangdp123120 • updated 16 days ago by Biostar ♦♦ 20
1
vote
1
answer
106
views
1
answer
The tools to plot the saturation curve for RNA-Seq
... 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 ...
rna-seq written 4 weeks ago by wangdp123120 • updated 4 weeks ago by Martombo2.3k
0
votes
1
answer
217
views
1
answers
Comment: C: "Segmentation fault" error from running align function in Rsubread package
... 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 wangdp123120
1
vote
1
answer
217
views
1
answer
"Segmentation fault" error from running align function in Rsubread package
... 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 ...
rsubread rna-seq written 9 weeks ago by wangdp123120 • updated 8 weeks ago by i.sudbery2.6k

Latest awards to wangdp123


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1838 users visited in the last hour