User: Antonio R. Franco

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Spain. Universidad de Córdoba
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Posts by Antonio R. Franco

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Comment: C: Installing samtools from sourceforge
... are you in the same directory that samtools is ? In addition... is the samtools file executable ?. You can see it by running ls -l You need to see an "x" at least in the first group of letters after the hyphen If not, run chmod +x samtools ...
written 14 hours ago by Antonio R. Franco3.9k
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Answer: A: Installing samtools from sourceforge
... It is likely you don't have the samtools executable binary in the $PATH. If so, try to run it by using ./samtools when you are in the directory containing the program ...
written 16 hours ago by Antonio R. Franco3.9k
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Answer: A: Per base GC content with a shoulder after adapter removal and trimming
... Shoulders in this graphics are usually compatible with at least two issues 1. Presence of contaminant DNA 2. Poor quality in the sequencing The point2 can be solved at least in part after a quality trimming. If the shoulder persist after the quality trimming a contamination fo your samples can be ...
written 12 days ago by Antonio R. Franco3.9k
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Comment: C: CpG Methylation data from PacBio sequencing
... Of course no. I was simply trying to indicate that if you don't add methylated precursors to your PCR it is impossible to include methylated bases to your DNA. And if you add such as methylated precursors they will not follow the original pattern in any case ...
written 13 days ago by Antonio R. Franco3.9k
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Answer: A: CpG Methylation data from PacBio sequencing
... Neither you add methylated precursors in the PCR to maintain that status. That will be worthless in any case ...
written 13 days ago by Antonio R. Franco3.9k
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Answer: A: design matrix for time point comparision [1 treatment] in time course RNA Seq -
... Why don't you use specialized R packages for time course such as [impulseDE2][1] or [maSigPro][2] [1]: https://www.bioconductor.org/packages/release/bioc/html/ImpulseDE2.html [2]: https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html ...
written 16 days ago by Antonio R. Franco3.9k
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Answer: A: How to use simultaneously long and short reads to assemble de novo a transcript
... Obviously it depends on the program you use [Oases][1] for example, uses categories or "channels" each one defined as long, short, paired, single, etc in the command lane. This let you use all kind of reads, and even a reference If compiled by default, you can use 2 of these categories. But you de ...
written 23 days ago by Antonio R. Franco3.9k
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Answer: A: Organizing tools/ software
... If working with Linux, copy the binaries in a path included into your path. I use to use /usr/local/bin You need to be superuser to be able to do it Another possibiity is to add the export PATH command in a file such as .bashrc that is read every time you initiate Linux. ...
written 24 days ago by Antonio R. Franco3.9k
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Answer: A: sequence alignment of protein sequence
... Give a try to [Clustal Omega][1] It is a global alignment program that uses a Hidden Markov Mode. [1]: https://www.ebi.ac.uk/Tools/msa/clustalo/ ...
written 28 days ago by Antonio R. Franco3.9k
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Comment: C: BLAST multiple database against each other
... Give details. What sort of database are you talking about? What is the query ? ...
written 4 weeks ago by Antonio R. Franco3.9k

Latest awards to Antonio R. Franco

Teacher 5 days 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 20 days 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 23 days 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 10 weeks ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For How to get native bash in Windows 10
Appreciated 6 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Student 6 months ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
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?
Scholar 7 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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 How to get native bash in Windows 10
Popular Question 9 months ago, created a question with more than 1,000 views. For How to get native bash in Windows 10
Teacher 10 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?
Epic Question 10 months ago, created a question with more than 10,000 views. For Can the code of a R package be changed? How?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Can I assemble a Eukaryote RNA-Seq using my laptop?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 13 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
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?
Popular Question 15 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
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 18 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Popular Question 18 months ago, created a question with more than 1,000 views. For Synchronization of fastq files
Great Question 19 months ago, created a question with more than 5,000 views. For Can the code of a R package be changed? How?
Scholar 23 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?

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