User: vincentpailler

gravatar for vincentpailler
Reputation:
140
Status:
Trusted
Location:
Last seen:
4 days ago
Joined:
1 year, 11 months ago
Email:
v*************@hotmail.fr

Posts by vincentpailler

<prev • 118 results • page 1 of 12 • next >
0
votes
1
answer
66
views
1
answers
Comment: C: Share FastQC results on GitLab
... I understand. But it could be possible to host the FastQC html file and make it visible by everyone? ...
written 5 days ago by vincentpailler140
0
votes
1
answer
66
views
1
answers
Comment: C: Share FastQC results on GitLab
... Thanks, I'm gonna check your work. ...
written 5 days ago by vincentpailler140
0
votes
1
answer
66
views
1
answers
Comment: C: Share FastQC results on GitLab
... Thanks for your anwer, I am going to check that tool. When I will have included the FastQC html file into my `.md` file, and I will have converted that .md file into a `.pdf` file, anyone would be able to open the link? ...
written 5 days ago by vincentpailler140
0
votes
1
answer
66
views
1
answer
Share FastQC results on GitLab
... Hello, I ran a FastQC analysis and get some results. I would like to share the `.html` results page on GitLab. The problem is that I downloaded that `.html` file , and it is located on my **C: disk**. I don't know if I can share that file on GitLab in a markdown file in order that other people c ...
fastqc html markdown gitlab written 5 days ago by vincentpailler140 • updated 5 days ago by Pierre Lindenbaum129k
1
vote
1
answer
65
views
1
answers
Answer: C: De novo alignement with smrttools
... Actually, to run this kind of smrttools pipeline, you need to insert a `cromwell.conf` file in the command line. It includes settings, paramaters ... I found a solution : I don't put the `HGAP_GenomeLength_str=13000000` in the command line but in that file. Cause even if I put the option `HGAP_Genom ...
written 11 days ago by vincentpailler140
1
vote
1
answer
65
views
1
answer
De novo alignement with smrttools
... Hello, I work with smrttools and the tools hgap4 to make a de novo alignement. This my command line : pbcromwell run pb_hgap4 -e /home/my.subreadset.xml --task-option HGAP_GenomeLength_str 13000000 --nproc 32 --config /home/cromwell.conf The problem is with the option `HGAP_GenomeLength_str` ...
alignment smrttools denovo written 11 days ago by vincentpailler140
0
votes
1
answer
871
views
1
answers
Comment: C: CheckM and strain heterogeneity
... I retried to use CheckM on another dataset, I get this result : ![checkM][1] I don't know what I have to think about my result. I do not have any contamination or any heterogeneity.. Does that mean that the bin correspond to related species ? And how do you calculate the completness of the differe ...
written 10 months ago by vincentpailler140
0
votes
1
answer
871
views
1
answers
Comment: C: CheckM and strain heterogeneity
... Thanks for the answer. They have a low completness because they have a very low contamination, right? For the moment, there is not a real proof of taxonomic unit ? And if yes, at what level? ...
written 10 months ago by vincentpailler140
0
votes
1
answer
871
views
1
answers
Comment: C: CheckM and strain heterogeneity
... Also, can we consider each bin here as a MAG? If yes, how do you consider a "good" MAG, or at least a bin which really corresponds to a real MAG? I read a paper that says a "real" MAG is a one with <10% contamination or completness is 5*contamination>50 . It looks right for you? ...
written 10 months ago by vincentpailler140
0
votes
1
answer
871
views
1
answers
Comment: C: CheckM and strain heterogeneity
... ![CheckM results][1] Thanks for your answer. It is more clear for me. If you look at my CheckM results, they look pretty bad or nonetheless, I can say that the bins found are unrelated and do not correspond to a same species, right? [1]: https://i.postimg.cc/hvPSHXCK/CheckM.png ...
written 10 months ago by vincentpailler140

Latest awards to vincentpailler

Popular Question 27 days ago, created a question with more than 1,000 views. For Salmon quantification vs HTSeq count quantification
Popular Question 7 months ago, created a question with more than 1,000 views. For Difference between HTSeq-count & Salmon quant results
Popular Question 10 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping
Centurion 12 months ago, created 100 posts.
Popular Question 16 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1492 users visited in the last hour