User: Antonio R. Franco
Antonio R. Franco • 4.4k
- Reputation:
- 4,410
- Status:
- Trusted
- Location:
- Spain. Universidad de Córdoba
- Last seen:
- an hour ago
- Joined:
- 5 years, 6 months ago
- Email:
- a*******@uco.es
Posts by Antonio R. Franco
<prev
• 604 results •
page 1 of 61 •
next >
0
votes
1
answer
21
views
1
answers
... Take a deep read of the [edgeR package][1], where is indicated what to do in your case
In addition. I cannot recall or ensure you can also use [Noiseq][2]
[1]: https://bioconductor.org/packages/release/bioc/html/edgeR.html
[2]: https://www.bioconductor.org/packages/release/bioc/html/NOISeq.htm ...
written 1 hour ago by
Antonio R. Franco • 4.4k
0
votes
2
answers
74
views
2
answers
... And beware of the using of "T" and "F" as they can be considered as TRUE and FALSE into R ...
written 8 days ago by
Antonio R. Franco • 4.4k
1
vote
2
answers
74
views
2
answers
... It it not important the way you name your factors as long as you can separate and group your samples. You can name factor as letters or as numbers
But at the time of doing the DE analysis, it matters the ORDER you define that factor when the DE analysis is requested. By default, DESEq2 order that f ...
written 8 days ago by
Antonio R. Franco • 4.4k
1
vote
1
answer
114
views
1
answers
... I don't think so.
Accession values or codes are (or should be) unique to each sequence. I don't catch this point, nor I have an adequate answer to explain this ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
0
votes
1
answer
114
views
1
answers
... If you are using the WEB NCBI service, go to the Algorithm parameter tab where you can see all of the options, like the match/mismatch scores, the word size (which differentiates a megablast from a dc-megablast), and the gap options which penalize gap creation and extension in a linear fashion or wi ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
0
votes
1
answer
114
views
1
answers
... To ensure the same results local and remotely, you should not only use the same kind of task (megablast or dc-megablast), but also the same gap and extension penalties, and the same score rule when bases coincide or not in the sequence ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
0
votes
1
answer
114
views
1
answers
... The species names can vary depending upon the way you search. By running a dc-blast, you use a smaller word in the searching than when using megablast, so you can fill out the list with less conserved sequences that lead to a different species list ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
2
votes
1
answer
114
views
1
answers
... I assume megablast is different that running a discontinuous blast (dc-megablast)
This is taken after running `blastn -help`
-task
Another source of variation could be the database used. The local one cannot necessarily coincide with the remote if the newest sequences are not included. I beli ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
0
votes
2
answers
137
views
2
answers
... Take a look to this lane. LogFoldChange is calculated as Log2
https://github.com/satijalab/seurat/blob/master/R/differential_expression.R#L1414 ...
written 4 weeks ago by
Antonio R. Franco • 4.4k
1
vote
4
answers
207
views
4
answers
... Another possibility:
If you know the bacterial genome, you have the chance to get rid from most of their sequences by filtering the reads by using [BBSplit][1]
Then, you need to assemble again with the filtered reads. Neither a mapping with bowtie or a filtering with BBSplit can guarantee you can ...
written 10 weeks ago by
Antonio R. Franco • 4.4k
Latest awards to Antonio R. Franco
Popular Question
29 days ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Student
8 weeks ago,
asked a question with at least 3 up-votes.
For How would you discover the source of contaminant DNA ?
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Scholar
5 months ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Good Answer
5 months ago,
created an answer that was upvoted at least 5 times.
For A: Can I assemble a Eukaryote RNA-Seq using my laptop?
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For The NAR annual Web Server Issue is here..
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Scholar
16 months ago,
created an answer that has been accepted.
For A: How to find the Genes present in the sequence?
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: Must know algorithms before attending a bioinformatics interview
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: is there any databse that provides the promoter of a specific gene?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Recommended coverage for methylome analysis
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1096 users visited in the last hour