User: Shaminur

gravatar for Shaminur
Shaminur40
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
Comment: C: How to extract genome from iontorent bam file?
... Thank you very much for your valuable succession. ...
written 13 days ago by Shaminur40
4
votes
2
answers
105
views
2
answers
Answer: A: How to extract genome from iontorent bam file?
... 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 Shaminur40
0
votes
2
answers
105
views
2
answers
Comment: C: How to extract genome from iontorent bam file?
... Thank you, can you please share the code, like align with bwa and then? ...
written 14 days ago by Shaminur40
10
votes
2
answers
105
views
8 follow
2
answers
How to extract genome from iontorent bam file?
... 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 ...
genome assembly alignment written 14 days ago by Shaminur40
1
vote
1
answer
236
views
1
answers
Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... 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 Shaminur40
0
votes
1
answer
236
views
1
answers
Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... Thank you dear Asaf, I am looking for this kind of resources. Really sorry for westing your valuable time. ...
written 8 weeks ago by Shaminur40
0
votes
1
answer
236
views
1
answers
Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... 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 Shaminur40
0
votes
1
answer
236
views
1
answers
Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... 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 Shaminur40
0
votes
1
answer
236
views
1
answers
Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... 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 Shaminur40
9
votes
1
answer
236
views
1
answer
Download all bacterial genome from Refseq in fasta format from NCBI
... 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 ...
genome written 8 weeks ago by Shaminur40

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.

Help
Access

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