User: Antonio R. Franco

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Spain. Universidad de Córdoba
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3 years, 3 months ago
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Posts by Antonio R. Franco

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Answer: A: Does STAR give the reads that were mapped at intergenic regions? How can I get t
... STAR does the mapping throughout all the genome, and places the reads from they derive. If you have reads fron intergenic regions, they will be mapped there.. I will think into several approaches FIRST ONE Map to the whole reference genome What you need is a reference gtf or gff file containing th ...
written 16 days ago by Antonio R. Franco3.5k
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Answer: A: finding contigs present in one assembly but missing from another
... Why don't you run a dotlet like program like those that are now being used for comparing a genome with an optical map ? I am refering to [DAGChainer][1]. Get the idea [from this paper][2] [1]: http://dagchainer.sourceforge.net/ [2]: https://academic.oup.com/gigascience/advance-article/doi/10.1 ...
written 18 days ago by Antonio R. Franco3.5k
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Answer: A: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
... Wondering if this or a similar approach can be taken for lectures coming from a stranded (dUTP) library.. ...
written 5 weeks ago by Antonio R. Franco3.5k
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Answer: A: Structure of a enzyme
... The only protein 3D database I am aware of is [PDB][1] [1]: https://www.rcsb.org/pdb/home/home.do ...
written 6 weeks ago by Antonio R. Franco3.5k
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Comment: C: gene expression and RNA-Seq
... I understand that theses premises are only valid for human transcriptomes.. ...
written 9 weeks ago by Antonio R. Franco3.5k
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Comment: C: Alignment of the partial genome sequencing
... You can look for SNP under different approaches 1. Look for samtools mpileup 2. Load the sam file along the reference genome in a visual genomic browser like IGV o IGB. The same can be done with samtools tview but in not such as elegant way 3. Look for the way of getting a VCF (variant file) usin ...
written 10 weeks ago by Antonio R. Franco3.5k
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Answer: A: Alignment of the partial genome sequencing
... with samtools view selected.sam | wc -l you count the number of mapped reads to this range,. There are 285 mapped reads ...
written 10 weeks ago by Antonio R. Franco3.5k
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Comment: C: Alignment of the partial genome sequencing
... I got your file.. Your bam file is right. It contains the header. I see you used bowtie2 with samtools view -H SRR733103.bam with samtools view SRR733103.bam | cut -f3 | uniq -c I can see that you have 3777516 mapped reads to the reference sequence named NC_006088.4 (is not chr1, you need to use ...
written 10 weeks ago by Antonio R. Franco3.5k
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Comment: A: Alignment of the partial genome sequencing
... You are doing right in reding these instructions [http://www.htslib.org/doc/samtools.html][1]. samttools view had some requirements, like the presence of the header. If you want, share your bam file with me through dropbox, mega or the like, and I give it a look. My address is arfranco (@) uco.es ...
written 10 weeks ago by Antonio R. Franco3.5k
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Answer: A: Alignment of the partial genome sequencing
... You have several choices 1. You can map all of your lectures to the whole reference genome, and thus, interrogate with samtools which of your lectures map to this region. samtools view accepted_hits.bam chr1:67246039-67350164 > mylectures.sam This order assumes that your bam mapped file is name ...
written 10 weeks ago by Antonio R. Franco3.5k

Latest awards to Antonio R. Franco

Teacher 5 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?
Epic Question 6 weeks ago, created a question with more than 10,000 views. For Can the code of a R package be changed? How?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Can I assemble a Eukaryote RNA-Seq using my laptop?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 4 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Teacher 5 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 6 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
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 9 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Popular Question 9 months ago, created a question with more than 1,000 views. For Synchronization of fastq files
Great Question 10 months ago, created a question with more than 5,000 views. For Can the code of a R package be changed? How?
Scholar 14 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Commentator 15 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 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?
Student 15 months ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
Scholar 15 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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?
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 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?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Can I assemble a Eukaryote RNA-Seq using my laptop?
Popular Question 19 months ago, created a question with more than 1,000 views. For Can the code of a R package be changed? How?
Scholar 20 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?

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