User: Antonio R. Franco

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Spain. Universidad de Córdoba
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Joined:
5 years, 6 months ago
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Posts by Antonio R. Franco

<prev • 604 results • page 1 of 61 • next >
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Answer: A: Dealing with only 2 samples in RNA-SEQ
... 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. Franco4.4k
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Comment: C: How to set group in EdgeR and DEseq2?
... 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. Franco4.4k
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Answer: A: How to set group in EdgeR and DEseq2?
... 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. Franco4.4k
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Comment: C: Different results between remote and online blast
... 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. Franco4.4k
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Comment: C: Different results between remote and online blast
... 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. Franco4.4k
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Comment: C: Different results between remote and online blast
... 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. Franco4.4k
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Comment: C: Different results between remote and online blast
... 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. Franco4.4k
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Answer: A: Different results between remote and online blast
... 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. Franco4.4k
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Comment: C: Question about logFC while using DESeq2 in Seurat
... 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. Franco4.4k
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Answer: A: How to assemble viral genomes when my data contains host DNA as well
... 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. Franco4.4k

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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

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