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User: Antonio R. Franco

gravatar for Antonio R. Franco
Reputation:
3,370
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Trusted
Location:
Spain. Universidad de Córdoba
Last seen:
7 hours ago
Joined:
2 years, 12 months ago
Email:
a*******@uco.es

Posts by Antonio R. Franco

<prev • 498 results • page 1 of 50 • next >
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Answer: A: Kallisto pseudobam to IGV
... In addition.. Is that bam as accurate and useful than those obtained with splicing aware mappers like STAR o HISAT ? ...
written 8 weeks ago by Antonio R. Franco • 3.4k
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Comment: C: HISAT2 rna-strandness option
... https://www.biostars.org/p/64250/ ...
written 10 weeks ago by Antonio R. Franco • 3.4k
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Answer: A: HISAT2 rna-strandness option
... This is sort of confusing. You need to organize the ideas.. You usually only read the "+" or 5' -> 3' strand of your reference genome **in a text file**. The "-" strand is usually hidden in that file. This information is important to acknowledge the orientation of your genome, and the direction ...
written 10 weeks ago by Antonio R. Franco • 3.4k
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Answer: A: HISAT2 rna-strandness option
... Because there are at least two main methods for the synthesis of cDNA in stranded libraries - the dUTP method preserves the complementary strand - the Illumina method that directly links to the RNA the linkers, preserves the original orientation of the RNA ![enter image description here][1] ![ent ...
written 10 weeks ago by Antonio R. Franco • 3.4k
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Comment: C: Gene Ontology Tool Selection
... the section for term enrichment tools has been discontinued... ...
written 11 weeks ago by Antonio R. Franco • 3.4k
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Comment: C: Using RPK counts as DESeq2 input
... RPKM, FPKM and TPM are methods for normalizing reads that relies on gene length and deep of sequencing But [in this video][1], you can see that DESeq2 uses a different normalization method that needs the raw counts as input [1]: https://www.youtube.com/watch?v=UFB993xufUU ...
written 4 months ago by Antonio R. Franco • 3.4k
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Comment: C: blastn for very short sequences
... I agree. Bowtie1 is a lot more sensitive than bowtie2 for such as short query sequences. Notice that bowtie1 will give you matched sequences that are not fully identical to your subject. You will need to play with grep looking for the NM tag to control the number of truly identical annealed bases ( ...
written 4 months ago by Antonio R. Franco • 3.4k
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Getting profit (plots, data) from my final GO enrichment analysis..
... I've done with a GO enrichment analysis after running a DE analysis, and ended with a file like this gene02308-v1.0-hybrid GO:0005773, GO:0006950 gene02380-v1.0-hybrid GO:2000033, GO:2000280 gene03187-v1.0-hybrid GO:0005739, GO:0006974, GO:0008270, GO:0009228, GO:0009409, GO:0009570, GO ...
go rna-seq plot written 4 months ago by Antonio R. Franco • 3.4k
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Comment: C: Bacterial de novo genome assembly
... Many other programs do it. In particular, Velvet and SOAP can use reference genomes to assist a de novo assembly. In my hands. the using of a trusted reference genome for assisting a de novo assembly, gave better results than a de novo assembly that was processed by Mauve afterwards ...
written 4 months ago by Antonio R. Franco • 3.4k
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Comment: C: Bacterial de novo genome assembly
... Not to forget that you can use a reference assisted assembly if you consider that a nice reference genome can be used for this purpose ...
written 5 months ago by Antonio R. Franco • 3.4k

Latest awards to Antonio R. Franco

Popular Question 9 days ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Teacher 7 weeks 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 3 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Teacher 4 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 5 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Popular Question 5 months ago, created a question with more than 1,000 views. For Synchronization of fastq files
Great Question 6 months ago, created a question with more than 5,000 views. For Can the code of a R package be changed? How?
Scholar 10 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Why mate-Paired end, Paired-end and Single End reads library to be combined for
Teacher 11 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?
Student 11 months ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
Scholar 11 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Teacher 11 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 13 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 14 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 15 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 15 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Good Answer 15 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 15 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 16 months ago, created a question with more than 1,000 views. For Can the code of a R package be changed? How?
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?
Scholar 16 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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 16 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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