User: Sissi
Sissi • 50
- Reputation:
- 50
- Status:
- Trusted
- Location:
- Italy
- Last seen:
- 1 day, 10 hours ago
- Joined:
- 5 years, 3 months ago
- Email:
- s********@gmail.com
Posts by Sissi
<prev
• 23 results •
page 1 of 3 •
next >
0
votes
1
answer
1.3k
views
1
answers
... I know it's been a while but maybe it could help someone else..
I got the same error and then I noticed that I was working as user in a folder with root permission.
Moved my folder into my home and everything worked well.
Cheers. ...
written 7 weeks ago by
Sissi • 50
0
votes
1
answer
169
views
1
answers
... That's perfect!!
What is the purrr::reduce doing??
Thank you very much guys! ...
written 8 weeks ago by
Sissi • 50
0
votes
1
answer
169
views
1
answers
... That's awesome! I should learn/use more often those three commands, thanks a lot! ...
written 8 weeks ago by
Sissi • 50
0
votes
1
answer
169
views
1
answers
... Oh sorry.
I edited the previous post.
That's one column (called COG_CATEGORY) of a CSV file with many more columns and thousands of raws, I copied just few to give an idea.
And that's what I would like:
A
A
B
B
B
R
R
R
Q
Q
Q
P
P
P
G
G
...
written 8 weeks ago by
Sissi • 50
3
votes
1
answer
169
views
1
answer
... Hi guys,
I have probably an easy task but my R knowledge is not good enough.
I have a column with COG-annotation categories, with some raws having multiple categories:
A
A
B|Q
B|Q
B|Q
R|P|G|E
R|P|G|E
R|P|G|E
I would like to split them (thus removing the | separator ...
written 8 weeks ago by
Sissi • 50
• updated
8 weeks ago by
bioinformatics2020 • 570
0
votes
0
answers
340
views
0
answers
Comment:
A: Unique genes roary
... Ok so,
1. NCBI annotation is not an option, because the newly sequenced
strain doesn not have the NCBI annotation yet and a combination of
NCBI+Prokka of course is not working.
2. Prokka + roary + query_pan_genome for strainX singletons gives 38
genes that are actually present in st ...
written 4 months ago by
Sissi • 50
0
votes
0
answers
340
views
0
answers
Comment:
A: Unique genes roary
... Following your suggestion, I tried to use the ncbi gff files and prokka gff file for the newly sequenced strain from Prokka, but first got:
Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix, new GFF in the fixed_input_files directory
and then stopped:
...
written 4 months ago by
Sissi • 50
0
votes
0
answers
340
views
0
answers
Comment:
A: Unique genes roary
... Hi Andres,
Thank you for your reply.
I first downloaded the FASTA file from NCBI genome ( [This is my Reference as example][1] ) and then run Prokka:
for k in *.fasta; do prokka $k --outdir /home/silvia/Pseudomonas/prokka/"$k" --kingdom Bacteria --genus Pseudomonas; done
This because I'm also ...
written 4 months ago by
Sissi • 50
0
votes
0
answers
340
views
0
answers
... Hi there,
I'm running a pangenome analyisis on 20 bacterial strains using roary version 3.13, on a server running CentOS 7.
I want to get the unique genes present in only one of those 20 strains but, as I've already asked [here][1], I cannot get them.
When running:
query_pan_genome -a differe ...
written 4 months ago by
Sissi • 50
0
votes
1
answer
1.0k
views
1
answers
Comment:
C: ballgown has "." as Gene Names
... Thank you very much.
I was also going to try exactly that pipeline but I did not want to leave the ballgown incomplete. :) ...
written 10 months ago by
Sissi • 50
Latest awards to Sissi
Popular Question
23 days ago,
created a question with more than 1,000 views.
For Velvet compilation error
Great Question
3.7 years ago,
created a question with more than 5,000 views.
For Samtools consensus sequence
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For BWA mapping with mismatches
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Samtools consensus sequence
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1752 users visited in the last hour