User: Andrew Watson

gravatar for Andrew Watson
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
1 month ago
Joined:
6 years, 11 months ago
Email:
a**************@gmail.com

about me

Posts by Andrew Watson

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
105
views
1
answers
Comment: C: OMA standalone estimating memory use for bacterial genomes
... Hi Adrian, Great, thanks for the information. I had thought/hoped that they might scale differently. I was mainly checking to get an idea of a starting point to discuss with the HPC admins. A single core with high memory and for a longer than usual wall-time doesn't fit neatly into any of their ...
written 4 weeks ago by Andrew Watson40
4
votes
1
answer
105
views
1
answer
OMA standalone estimating memory use for bacterial genomes
... I am trying to estimate memory requirements to run the final steps OMA standalone (after the ALL-vs ALL) on a HPC (slurm), without HOG inference. From the benchmarks in the manual, the suggested formula is 400MB * pow(nr_genomes, 1.4). This works for the described metazoan dataset (60 metazoas hav ...
orthologs oma written 4 weeks ago by Andrew Watson40 • updated 4 weeks ago by adrian.altenhoff700
0
votes
1
answer
1.5k
views
1
answers
Answer: A: phylobayes mpi error
... I was under the impression that Phylobayes only accepts .phy files so did not think of this until I asked around. If anyone is still having this problem then it can be easily worked around by inputting the sequence in .nexus format, so that the data type is explicitly stated. ...
written 4.5 years ago by Andrew Watson40
0
votes
1
answer
1.5k
views
1
answers
Comment: C: phylobayes mpi error
... We are having the same error. Has this been resolved? We have been running pb_mpi on two linux servers successfully for some time now. The error occurred with a new alignment, but we went back to check some older ones we have successfully used in the past with pb_mpi and came up against the same e ...
written 4.5 years ago by Andrew Watson40
0
votes
11
answers
163k
views
11
answers
Comment: C: Tools To Calculate Average Coverage For A Bam File?
... Very useful thanks! Used it on my own dataset (sorry to bump an old thread but still very handy) ...
written 6.7 years ago by Andrew Watson40
2
votes
1
answer
3.8k
views
1
answers
Answer: A: Cummerbund Expressionbarplot Na/Infinite Error
... Just to confirm I have been managed to solve this in case anyone else encounters the problem. As I have annotated against a reference genome I have some cases where zero expression has been detected under either of the conditions I am studying. I used the matrix of the fpkm values (from fpkmMatrix ...
written 6.9 years ago by Andrew Watson40
3
votes
1
answer
3.8k
views
1
answer
Cummerbund Expressionbarplot Na/Infinite Error
... Hi all, I am having trouble with the expressionBarplot function on cummeRbund and was wondering if anyone could help me. I want to look at the expression plot of a manually created geneset. I have worked through several already without any problems, but this particular set is pulling up the below ...
rnaseq cummerbund written 6.9 years ago by Andrew Watson40

Latest awards to Andrew Watson

Popular Question 6.0 years ago, created a question with more than 1,000 views. For Cummerbund Expressionbarplot Na/Infinite Error

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2035 users visited in the last hour