User: fhsantanna
fhsantanna • 490
- Reputation:
- 490
- Status:
- Trusted
- Location:
- Brazil
- Last seen:
- 2 weeks, 4 days ago
- Joined:
- 6 years, 8 months ago
- Email:
- f*********@yahoo.com.br
Posts by fhsantanna
<prev
• 154 results •
page 1 of 16 •
next >
0
votes
1
answer
154
views
1
answers
... I found the problem. I was actually comparing results of different versions of ivar, 1.1 and 1.3. The last version was introducing more N's in the consensus, because it demands a depth of 10x for calling a base. ...
written 28 days ago by
fhsantanna • 490
0
votes
1
answer
154
views
1
answers
... This was actually a good idea. I identified a region that was different between the assembly approaches. This region presents a depth mode of 3X, it was included in the original protocol, but removed when I utilized the -e option of ivar. Interestingly, the first two bases of this region presents a ...
written 28 days ago by
fhsantanna • 490
0
votes
1
answer
154
views
1
answers
... Yes, if I utilize the -e option reads that don't have primers are kept. Since amplicons are fragmented during QIASeq procedure, some DNAs of the library pool probably will not have primer sites.
Reads without primers are removed by default by ivar.
The only program that could influence the procedure ...
written 29 days ago by
fhsantanna • 490
0
votes
1
answer
154
views
1
answer
... I am following the workflow of Erin Young ([https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/BFX-UT_ARTIC_Illumina][1]) for assembly of the genomes of SARS-Cov-2.
For sequencing the genomes, we utilized the QIAseq Library kit, which is based on ARTIC workflow, and the Illumina p ...
written 4 weeks ago by
fhsantanna • 490
0
votes
0
answers
291
views
0
answers
... Spades is for de novo assembly, isn't it? Wouldn't a reference based assembly method be faster? ...
written 6 months ago by
fhsantanna • 490
0
votes
0
answers
291
views
0
answers
... Yes, Kevin. It is the ampliseq panel for SARS-CoV-2. Could you please give me more details about it?
I have inquired the technical support the same question, but they responded that we would have to use basespace. ...
written 6 months ago by
fhsantanna • 490
4
votes
0
answers
291
views
0
answers
... Do you have a protocol using open source software for assembling SARS-CoV-2 genome sequences after Ampliseq sequencing?
...
written 6 months ago by
fhsantanna • 490
• updated
6 months ago by
GenoMax ♦ 94k
0
votes
0
answers
142
views
0
answers
... I am working with a genome sequence of a bacterial thermophile.
Its genome seems to be very "chimeric", because the best-hits of each gene are from different taxonomic groups.
Do you know a program to plot the genome and color its genes based on taxonomy? Something like this picture: ![https://www.n ...
written 8 months ago by
fhsantanna • 490
0
votes
0
answers
285
views
0
answers
... Searching in the literature I find these terms as synonyms, but also as different processes. After all, are these terms equivalent? ...
written 17 months ago by
fhsantanna • 490
0
votes
1
answer
481
views
1
answers
... Thank you very much. As I thought, it seems only a nomenclature divergence for the same thing. ...
written 18 months ago by
fhsantanna • 490
Latest awards to fhsantanna
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Why some genomes are not available in genbank ftp?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For gbk2faa: why is it not working for refseq gbk?
Epic Question
17 months ago,
created a question with more than 10,000 views.
For Extract fasta sequences from a large file using a list of names
Popular Question
17 months ago,
created a question with more than 1,000 views.
For gbk2faa: why is it not working for refseq gbk?
Great Question
17 months ago,
created a question with more than 5,000 views.
For How do I access genome coverage using SPADES?
Great Question
19 months ago,
created a question with more than 5,000 views.
For How do I access genome coverage using SPADES?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For gbk2faa: why is it not working for refseq gbk?
Popular Question
22 months ago,
created a question with more than 1,000 views.
For gbk2faa: why is it not working for refseq gbk?
Popular Question
22 months ago,
created a question with more than 1,000 views.
For DOOR2 (operon predictor) does not load my fna file, do you know an alternative software?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For gbk2faa: why is it not working for refseq gbk?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Epic Question
2.8 years ago,
created a question with more than 10,000 views.
For Best software to assemble bacterial genomes
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Metagenomic read recruitment: best software
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Software to display draft genome statistics
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Genbank submission error: ERROR: valid [SEQ_FEAT.CDSproductPackagingProblem] Protein product not packaged in nuc-prot set with nucleotide
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Metagenomic read recruitment: best software
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Spades assembler artifacts? Contigs containing long nt stretches.
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Software to display draft genome statistics
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Genbank submission error: ERROR: valid [SEQ_FEAT.CDSproductPackagingProblem] Protein product not packaged in nuc-prot set with nucleotide
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For How to create a Venn diagram using ortholog clusters?
Great Question
3.3 years ago,
created a question with more than 5,000 views.
For Extract fasta sequences from a large file using a list of names
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2035 users visited in the last hour