User: Antonio R. Franco

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Location:
Spain. Universidad de Córdoba
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3 hours ago
Joined:
3 years, 1 month ago
Email:
a*******@uco.es

Posts by Antonio R. Franco

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Comment: C: gene expression and RNA-Seq
... I understand that theses premises are only valid for human transcriptomes.. ...
written 1 day ago by Antonio R. Franco3.4k
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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 8 days ago by Antonio R. Franco3.4k
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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 9 days ago by Antonio R. Franco3.4k
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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 9 days ago by Antonio R. Franco3.4k
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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 9 days ago by Antonio R. Franco3.4k
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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 days ago by Antonio R. Franco3.4k
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Comment: A: Alignment of the partial genome sequencing
... Do you want to align only 1 chr1 sequence to the reference genome? Is that your question ? ...
written 10 days ago by Antonio R. Franco3.4k
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Comment: A: Obtain fragments from RNA-Seq reads?
... I don't understand what you are asking.. Can you clarify your question ? ...
written 18 days ago by Antonio R. Franco3.4k
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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 3 months ago by Antonio R. Franco3.4k
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Comment: C: HISAT2 rna-strandness option
... https://www.biostars.org/p/64250/ ...
written 4 months ago by Antonio R. Franco3.4k

Latest awards to Antonio R. Franco

Appreciated 9 days ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Teacher 3 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 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 7 months ago, created a question with more than 1,000 views. For Cuffcompare. Differences between class codes "=" and "i"
Popular Question 7 months ago, created a question with more than 1,000 views. For Synchronization of fastq files
Great Question 8 months ago, created a question with more than 5,000 views. For Can the code of a R package be changed? How?
Scholar 12 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
Commentator 12 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 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?
Student 13 months ago, asked a question with at least 3 up-votes. For Is qPCR actually required for RNA-Seq validation ?
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?
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 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?
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?
Good Answer 17 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 17 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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?
Popular Question 17 months ago, created a question with more than 1,000 views. For Can the code of a R package be changed? How?
Scholar 18 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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?
Scholar 18 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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?

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