User: Antonio R. Franco

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Spain. Universidad de Córdoba
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5 years ago
Email:
a*******@uco.es

Posts by Antonio R. Franco

<prev • 577 results • page 1 of 58 • next >
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Answer: A: edgeR gives no DE genes <0.05 FDR
... Run a PCA assay to test whether samples are differentiated or not. Sometimes samples are mixed up. My sequencing company sent me a treated sample as control and viceversa. With only that screwed sample in a triplicated experiment, I could not get any differential expression ...
written 9 hours ago by Antonio R. Franco4.1k
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Comment: C: Galaxy DE lncRNA analysis pipeline
... Here you have a tutorial.. [Tutorial HISAT SringTie Ballgown under R][1] In addition [Nature´s detailed protocol][2] [1]: https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/ [2]: https://www.ncbi.nlm.nih.gov/pubmed/27560171 ...
written 4 days ago by Antonio R. Franco4.1k
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Answer: A: TPM or FPKM for single cell RNA seq experiment ?
... It depends.. If you want to analyze differential expression with packages such as DESeq2 oe EdgeR, you need to provide the raw counts, since these packages has their own normalization methods ...
written 5 days ago by Antonio R. Franco4.1k
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Comment: C: neanderthals VCF file
... The genoma.fa file is the fasta file used as reference for the mapping to generate the BAM file ...
written 28 days ago by Antonio R. Franco4.1k
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Answer: A: How to process Illumina MiSeq paired-end reads for analysis
... I am wondering why you need to merge the two files. Most of program and resources are able to handle fastq file by separate. In addition, if using trimmers like Trim-galore or the like, you can ensure that both files are "synchronized" automatically The processing of paired-end reads is easy. In ...
written 4 weeks ago by Antonio R. Franco4.1k
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Answer: A: neanderthals VCF file
... Having the BAM file, you can generate a VCF file with samtools samtools mpileup -v -u -f genome.fa your.bam > variants.vcf ...
written 4 weeks ago by Antonio R. Franco4.1k
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Answer: A: When I run the tophat, the following error is given to me. How can I fix this er
... After reading the log, it is clear you don't have a problem with TopHat, This program ran the aligment All of the problem comes afterward, when using samtools ...
written 6 weeks ago by Antonio R. Franco4.1k
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Answer: A: How can I compare two reference genome
... Give a try to programs like [Mauve][1] [1]: http://darlinglab.org/mauve/user-guide/introduction.html ...
written 5 months ago by Antonio R. Franco4.1k
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Comment: C: Need Oligo6 software
... And Oligo 7 is out since a lot of time ago.. ...
written 6 months ago by Antonio R. Franco4.1k
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Answer: A: Integrating DMR data
... If you provide a gft file (or a gff file converted to a gtf), and a BED file, a nice option is to use [rgmatch.py][1] This program only needs a simple command lane documented in the web page, and gives you the position of the DMR (or any other feature) in the many places you choose, such as Upstrea ...
written 6 months ago by Antonio R. Franco4.1k

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Scholar 11 months ago, created an answer that has been accepted. For A: How to find the Genes present in the sequence?
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?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
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Teacher 12 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 12 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 12 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 14 months ago, created a question with more than 1,000 views. For Recommended coverage for methylome analysis
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Scholar 19 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 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?
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Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Can I assemble a Eukaryote RNA-Seq using my laptop?

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