User: Antonio R. Franco

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Spain. Universidad de Córdoba
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a*******@uco.es

Posts by Antonio R. Franco

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Comment: C: K-mer analysis meaning
... you need to investigate the using of the de Bruijn graph to explain this. Certainly, the assembling of genomes using kmers can at least in some cases have certain adventages over the assembling done using the overlapping method ...
written 2 days ago by Antonio R. Franco4.5k
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Help in interpreting an haploid assembled genome analyzed through BUSCO
... We have assembled HiFi PacBio reads with an haploid-aware assembler (hifiasm). It is a tree genome After analyzing the over 7900 contigs we got (expected genome size of 1,8Gb), we got these results obtained after using BUSCO, where it can be seen a very high number of duplicated sequences ![BUSCO a ...
busco assembling written 3 days ago by Antonio R. Franco4.5k • updated 3 days ago by lieven.sterck9.4k
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Answer: A: What is the difference between Structural variants and Structural Variation
... I would say the first is plural and the second singular They are the same concept ...
written 8 days ago by Antonio R. Franco4.5k
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Comment: C: Determination the KO numbers for the genes
... Of course. Give it a try ...
written 9 days ago by Antonio R. Franco4.5k
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Answer: A: Determination the KO numbers for the genes
... Look into KEGG by prior selection of your organism If you have the protein sequences and cann't find the KO codes, look for [BlastKoala][1] which is a tool included into KEGG to annotate them [1]: https://www.kegg.jp/blastkoala/ ...
written 9 days ago by Antonio R. Franco4.5k
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Comment: C: Next generation sequencing methodology
... One cluster gives you a read. The genome is attained after using an assemble program ...
written 20 days ago by Antonio R. Franco4.5k
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Comment: C: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
... Any odd flag has the byte 1 on because paired end reads were used in the mapping Obviously any even flag number means you were mapping single reads ...
written 20 days ago by Antonio R. Franco4.5k
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Comment: C: Detecting Novel Spliceforms from RNAseq data- Will STAR>RSEM work or do I need t
... If you have already your Illumina reads, and try to map to the reference genome, you need an splice aware mapper such as HISAT2 or STAR to unravel the junctions. You are comparing reads coming from mature RNA without introns with a reference genome that have them. ...
written 29 days ago by Antonio R. Franco4.5k
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Answer: A: Detecting Novel Spliceforms from RNAseq data- Will STAR>RSEM work or do I need t
... This would not be told a year ago... I would go to run IsoSeq sequencing with PacBio HiFi to answer this question Why? 1. Prices for PacBio sequencing has dropped dramatically. If can be pretty similar to that of Illumina nowdays 2. IsoSeq sequencing involves the true sequencing of your RNA popu ...
written 29 days ago by Antonio R. Franco4.5k
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Answer: A: qPCR to validate gene FPKM is 0 in RNA-Seq
... The problem here is how interpret these differences. I understand from your table that your RNA-Seq indicates that there is not expression of your genes, whereas the qPCR indicates that this not true. What of these two pieces of information shall we trust? In my opinion, RNA-Seq contains a trusted ...
written 11 weeks ago by Antonio R. Franco4.5k

Latest awards to Antonio R. Franco

Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Recommendations for bacterial data integration and/or System Biology
Great Question 4 months ago, created a question with more than 5,000 views. For Is qPCR actually required for RNA-Seq validation ?
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 4 months ago, created a question with more than 1,000 views. For Recommendations for bacterial data integration and/or System Biology
Scholar 7 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Popular Question 10 months ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Scholar 10 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Student 11 months ago, asked a question with at least 3 up-votes. For How would you discover the source of contaminant DNA ?
Popular Question 12 months ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Scholar 13 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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?
Scholar 13 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Scholar 13 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Scholar 14 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Appreciated 14 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 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?
Popular Question 17 months ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For The NAR annual Web Server Issue is here..
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Scholar 2.2 years ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Teacher 2.2 years 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 2.2 years ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview

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