User: Shaminur
Shaminur • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Dhaka University
- Last seen:
- 3 days, 5 hours ago
- Joined:
- 7 months, 3 weeks ago
- Email:
- m*****************@gmail.com
BS Hon's and MS in Microbiology, Department of Microbiology, University of Dhaka.
Posts by Shaminur
<prev
• 27 results •
page 1 of 3 •
next >
0
votes
2
answers
105
views
2
answers
... Thank you very much for your valuable succession. ...
written 13 days ago by
Shaminur • 40
4
votes
2
answers
105
views
2
answers
... This works for me
bwa mem ref.fa output.fq.gz > alignment.sam
samtools view -bS alignment.sam > aln.bam
samtools sort -m 2G aln.bam -o aln.sorted.bam
samtools mpileup -uf ref.fa aln.sorted.bam | bcftools call -c | vcfutils.pl vcf2fq -d 2 > cons.fa
Thank you
...
written 14 days ago by
Shaminur • 40
0
votes
2
answers
105
views
2
answers
... Thank you, can you please share the code, like align with bwa and then? ...
written 14 days ago by
Shaminur • 40
10
votes
2
answers
105
views
8 follow
2
answers
... Hi,
I hope everything is fine. I have a bam file with the COVID-19 genome from the ion torrent sequencing platform. I want to assemble them and tried with spades, But there is not enough read to form a contig. In that case, I want to assemble them with having gap (NNN). Is there any tools or pipeli ...
written 14 days ago by
Shaminur • 40
1
vote
1
answer
236
views
1
answers
... So far I learn, kraken2 prepare database directly from NCBI. The GTDB is a very good server for bacterial and archeal database. These two database will fulfill all my requiremen.
I am very greatful to you all. ...
written 8 weeks ago by
Shaminur • 40
0
votes
1
answer
236
views
1
answers
... Thank you dear Asaf, I am looking for this kind of resources. Really sorry for westing your valuable time. ...
written 8 weeks ago by
Shaminur • 40
0
votes
1
answer
236
views
1
answers
... Thank you, dear, You are right. But the `ncbi-genome-download -F fasta bacteria` downloaded each genome in each separate file and inside this file, it creates .fna.gz file. I was working in a server, that's why I can not recognize it.
So, now my point is each genome in each folder compressed .fna.g ...
written 8 weeks ago by
Shaminur • 40
0
votes
1
answer
236
views
1
answers
... Thank you very much, dear Vkkodali, So, you want to tell us that we need to download and merge those files into a single file. Here I have download all bacterial genome accordingly `(ncbi-genome-download -F fasta bacteria)` and try to merge them as cat command `(cat *.fna > all.fasta)`. But err ...
written 8 weeks ago by
Shaminur • 40
0
votes
1
answer
236
views
1
answers
... Thank you, dear Asaf. But want to prepare a database for metagenomic analysis, I wish, all the bacterial genome in a **single** file and Fasta format. I have also tried `ncbi-genome-download -F fasta bacteria` but it produces a single file for each genome. ...
written 8 weeks ago by
Shaminur • 40
9
votes
1
answer
236
views
1
answer
... How can I download all bacterial genome from RefSeq in Fasta format from NCBI in a single file? I want to download it in a server, so the Linux command will be more helpful.
Thanks in Advance
...
written 8 weeks ago by
Shaminur • 40
Latest awards to Shaminur
Teacher
13 days ago,
created an answer with at least 3 up-votes.
For A: How to extract genome from iontorent bam file?
Scholar
14 days ago,
created an answer that has been accepted.
For A: How to extract genome from iontorent bam file?
Supporter
8 weeks ago,
voted at least 25 times.
Autobiographer
8 weeks 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: 1683 users visited in the last hour