User: Optimist
Optimist • 160
- Reputation:
- 160
- Status:
- Trusted
- Location:
- Last seen:
- 4 hours ago
- Joined:
- 4 years ago
- Email:
- c************@gmail.com
Posts by Optimist
<prev
• 78 results •
page 1 of 8 •
next >
0
votes
1
answer
56
views
1
answers
... This worked
Thanks a ton ...
written 22 hours ago by
Optimist • 160
0
votes
1
answer
56
views
1
answers
... I want to know what command can be used to achieve the purpose.
It can be seqkit or anything else
...
written 22 hours ago by
Optimist • 160
4
votes
1
answer
56
views
1
answer
... My fasta header looks like this
>name1
ATGCATGCAT
My output must look like this
>alfaAB
--kv file looks like this
name1 alfaAB
What command can be used to achieve this??
Thank You
...
0
votes
3
answers
12k
views
3
answers
... I want to replace orf05188 with geneA ...
written 23 hours ago by
Optimist • 160
0
votes
3
answers
12k
views
3
answers
... Hi Shenwei
seqkit replace -k acc2gi.tsv -p "^(.+?) (.+)$" -r "gi|{kv}|ref|\$1| \$2" seqs.fasta > seqs.renamed.fasta
Can you modify this command for me?
This is my fasta header
>orf05188 draft|P. aeruginosa 908|Pseudomonas|orf05188 Scaffold_1 5479915 5478419 len=1497
My output h ...
0
votes
0
answers
108
views
0
answers
... Hi Biostars,
I have CARD-RGI outputs (.txt & .json) for multiple genomes.
Is there a tool or a python script that can combine these multiple outputs into 1 summary file. Maybe presence absence file or something like that.
Thank you ...
written 29 days ago by
Optimist • 160
0
votes
3
answers
154
views
3
answers
... Thank you
This might not help because most of the 16S rRNA seqs would be conserved (identical). ...
written 4 weeks ago by
Optimist • 160
2
votes
3
answers
154
views
3
answers
... I have found a solution to this.
seqkit rmdup -n -i -j > outfilename
Thank you all for the responses
Cheers
Have a great time!!! ...
0
votes
3
answers
154
views
3
answers
... This has worked too. Thank You
is there a way to remove duplicate headers along with the associated fasta sequence
Looks like most of the genomes have more than 1 16SrRNA sequences (as expected).
...
written 4 weeks ago by
Optimist • 160
0
votes
3
answers
154
views
3
answers
... filter_fasta.py has worked.
...
written 4 weeks ago by
Optimist • 160
Latest awards to Optimist
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Finding of origin of replication in a bacterial Genome
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Intall local BLAST in Ubuntu
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How to generate Protein Table file ( .ptt ) and RNA table file ( .rnt ) from a nucleotide fasta file?
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Finding of origin of replication in a bacterial Genome
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Supporter
21 months ago,
voted at least 25 times.
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Autobiographer
3.6 years ago,
has more than 80 characters in the information field of the user's profile.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1156 users visited in the last hour