User: Gautier Richard
Gautier Richard • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- MPI IE, Freiburg, Germany
- Website:
- https://www.linkedin.c...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 19 hours ago
- Joined:
- 1 month ago
- Email:
- g****************@gmail.com
Posts by Gautier Richard
<prev
• 30 results •
page 1 of 3 •
next >
0
votes
1
answer
99
views
1
answers
...
Your best chance is to use FIMO from the MEME suite and compare your sequence to the Chicken DNA Binding Protein Motifs Databases.
http://meme-suite.org/doc/fimo.html
I recommend using a Galaxy version of FIMO if you are not familiar with command-line tools.
One issue is that MEME doesn't have a ...
written 2 days ago by
Gautier Richard • 240
0
votes
4
answers
251
views
4
answers
... If you sort first I guess the chance is very small no? ...
written 15 days ago by
Gautier Richard • 240
0
votes
0
answers
117
views
0
answers
... I think it is a good way. Just ask how to increase the memory amount allowed to your job to your local bioinformaticians / cluster (HPC) managers. With the **Slurm** job manager (sbatch or SlurmEasy to launch scripts) this can be easily done at the beginning of the shell script you use to launch bow ...
written 16 days ago by
Gautier Richard • 240
0
votes
0
answers
117
views
0
answers
... It seems that you run out of memory. ...
written 17 days ago by
Gautier Richard • 240
0
votes
0
answers
112
views
0
answers
... Following this link you'll find a paper explaining how to use EdgeR and how to properly set a contrast matrix that will help you making the correct comparisons:
https://f1000research.com/articles/5-1408/v3
If you don't do KO1 vs KO2 or KO2 vs OE1 comparisons, perhaps it is better to only consider ...
written 20 days ago by
Gautier Richard • 240
0
votes
0
answers
109
views
0
answers
Comment:
C: How to plot gene cluster
... IGV should do the trick no? Are these sequences next to each other?
If not, you can rely on pyGenomeTracks to plot each sequence next to each other in a nice and automated manner:
https://github.com/deeptools/pyGenomeTracks
Otherwise, you can use illustrator or Inkscape if you want to just do it f ...
written 20 days ago by
Gautier Richard • 240
0
votes
2
answers
18k
views
2
answers
... Fragment Length usually corresponds to the size of the DNA or RNA fragments that have been sequenced. Such information is usually obtained with a Bioanalyzer. It can also be infered from the distance between pairs when performing paired-end sequencing. ...
written 21 days ago by
Gautier Richard • 240
3
votes
1
answer
122
views
1
answers
... Per base bedgraph should be of the following format:
Chr1 0 1 0.846
Chr1 1 2 0.745
Chr1 2 3 0.433
Chr1 3 4 0.313
Then you can convert it to bigwig easily using `bedGraphToBigWig` from UCSCTools.
Having your "custom file" should help us to guide you about how to get the bedgraph ...
written 21 days ago by
Gautier Richard • 240
1
vote
0
answers
140
views
0
answers
Comment:
C: Analysis pipeline for 3e Hi-C
... The idea might be to increase the resolution of Restriction Fragment length binned Hi-C matrices.
More restriction sites = smaller bins = higher resolution. I don't know if it helps them to identify new features though. ...
written 22 days ago by
Gautier Richard • 240
0
votes
0
answers
140
views
0
answers
Comment:
C: Analysis pipeline for 3e Hi-C
... I guess that since they know the restriction site of these 3 enzymes, instead of keeping reads with the pairs having the usual DpnII or HindIII restriction site, they looked for pairs showing either one of the 3 restriction sites? ...
written 24 days ago by
Gautier Richard • 240
Latest awards to Gautier Richard
Supporter
28 days ago,
voted at least 25 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2004 users visited in the last hour