User: Sissi

gravatar for Sissi
Sissi50
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
Answer: A: "Error creating sorted mer list" with progressiveMauve
... 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 Sissi50
0
votes
1
answer
169
views
1
answers
Comment: C: Split and recombine columns with R
... That's perfect!! What is the purrr::reduce doing?? Thank you very much guys! ...
written 8 weeks ago by Sissi50
0
votes
1
answer
169
views
1
answers
Comment: C: Split and recombine columns with R
... That's awesome! I should learn/use more often those three commands, thanks a lot! ...
written 8 weeks ago by Sissi50
0
votes
1
answer
169
views
1
answers
Comment: A: Split and recombine columns with R
... 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 Sissi50
3
votes
1
answer
169
views
1
answer
Split and recombine columns with R
... 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 ...
R awk cog cog annotation annotation written 8 weeks ago by Sissi50 • updated 8 weeks ago by bioinformatics2020570
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 Sissi50
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 Sissi50
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 Sissi50
0
votes
0
answers
340
views
0
answers
Unique genes roary
... 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 ...
comparative genomics pangenome roary written 4 months ago by Sissi50
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 Sissi50

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

Help
Access

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
_