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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Clustal Omega and bootstrapping
... I run Clustal Omega to get a cladogram Clustal Omega uses a HMM algorithm to cluster sequences together By the other hand, there are many programs to run bootstrapping with the alignments. One os such is IQ-Tree, which is fast, sensitive, and available locally or through a WEB server However, I d ...
clustal alignment bootstrap iq-tree written 9 days ago by Antonio R. Franco3.6k
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Answer: A: short RNA reads alignment
... The database you align with depends on your interest. Choose the best suitable for your purpose since you can map virtually with any sequences you want In relation to size, [take a look to this thread][1]. You can do it and even change some settings for your interest [1]: https://www.biostars.or ...
written 13 days ago by Antonio R. Franco3.6k
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Comment: C: Remove singletons from bam
... If you have this error when running the samtools command is that the original file is corrupted. If dealing with the final filtered file, give it a little time to finish the command. I have just tested the command and is working nicely ...
written 16 days ago by Antonio R. Franco3.6k
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Answer: A: Remove singletons from bam
... Take a look to this page [https://broadinstitute.github.io/picard/explain-flags.html][1] Then try to use samtools view with the -f and the -F options to select those mapped reads that are of your interest. If you have mapped paired reads, all your BAM flags will be an odd number, meaning that they ...
written 16 days ago by Antonio R. Franco3.6k
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Answer: A: Preparing primary assembly in RNAseq
... The first one is the fasta file corresponding to the genome The second one is the annotation of the first file I don't understand your third question. Significance of preparing for primary assembly in RNASequencing? These files are already assembled.. If you want to assemble again, you need to use ...
written 16 days ago by Antonio R. Franco3.6k
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Can you get information about variance of microarrays experiments from a MA plot ?
... Can you actually get this kind of information from a MA plot ? > The plot suggests that the variance of the individual transcriptomic > experiments is high and that a high number of genes in the plot > biological replicates show high standard deviations and are out of the > range for re ...
ma plot microarray written 20 days ago by Antonio R. Franco3.6k • updated 20 days ago by Devon Ryan78k
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Comment: C: Big news from Microsoft. BASH on windows.
... To date (March 2018) you can install a GUI into your WSL (WSL is the Windows Linux System without problems. Several links [like this one][1] can be followed [1]: https://github.com/Microsoft/WSL/issues/637 ...
written 5 weeks ago by Antonio R. Franco3.6k
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Comment: C: Is it normal a substantial reduction of BAM files after ordering ?
... I mentioned that. I am mapping BS-Seq sequences with Bismark ...
written 7 weeks ago by Antonio R. Franco3.6k
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Answer: A: Is it normal a substantial reduction of BAM files after ordering ?
... You are right. They have the same number of reads ...
written 7 weeks ago by Antonio R. Franco3.6k
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Is it normal a substantial reduction of BAM files after ordering ?
... I am getting BAM files with Bismark mapping with bowtie2. This gives you an unordered BAM file Thus, I am sorting the BAM file with the command > samtools sort -O bam -T tmp_ -o Name_sorted.bam Unordered.bam The unordered bam file can have a 2,6Gb size, but the ordered one drops down to 1,2Gb. ...
bam samtools written 7 weeks ago by Antonio R. Franco3.6k

Latest awards to Antonio R. Franco

Appreciated 13 days ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Student 29 days ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Teacher 6 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?
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 11 weeks ago, created a question with more than 1,000 views. For How to get native bash in Windows 10
Popular Question 3 months ago, created a question with more than 1,000 views. For How to get native bash in Windows 10
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?
Epic Question 4 months ago, created a question with more than 10,000 views. For Can the code of a R package be changed? How?
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?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 7 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Teacher 8 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 10 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
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?
Popular Question 12 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Popular Question 13 months ago, created a question with more than 1,000 views. For Synchronization of fastq files
Great Question 13 months ago, created a question with more than 5,000 views. For Can the code of a R package be changed? How?
Scholar 17 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Commentator 18 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 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?
Student 18 months ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
Scholar 18 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Teacher 19 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 20 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?

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