User: RafaelMP

gravatar for RafaelMP
RafaelMP110
Reputation:
110
Status:
Trusted
Location:
Brazil
Last seen:
4 days, 5 hours ago
Joined:
4 years, 10 months ago
Email:
r***************@gmail.com

PhD

Evolution, functional genomics, expression analysis and metabolic and structural analysis.

Posts by RafaelMP

<prev • 9 results • page 1 of 1 • next >
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edgeR - DE with one disease sample vs. multiple control samples?
... Hello! I am trying to use RNA-seq data to accomplish two objectives in a case vs. control study: 1 - Verify if the expression level is distinct between the case sample and the controls. 2 - We need to identify DE genes between conditions. Unfortunately, we have only one case with the mutation, bu ...
R next-gen rna-seq sequencing written 3 months ago by RafaelMP110 • updated 3 months ago by Gordon Smyth780
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Functional Genes x Pseudogenes
... Hi All, I am working with evolution of proteins in the human genome and I wanna know if is possible to obtain a list of all pseudogenes (human and non-human) with relationship with human genes. I did a test with gencode data (release 21), however there is only information about genes and pseudogene ...
pseudogenes database gencode human written 4.6 years ago by RafaelMP110 • updated 4.6 years ago by Siva1.6k
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How to download a large amount of NGS metadata for studies?
... Hi All, I am starting my project with RNA-Seq in human. I've worked with SRA data for other species, but the present work is much bigger. I do not know if there is a site that provides the information I want. I want to get two tables (txt or CSV) of experiments (with information to download the fi ...
next-gen control condition de rna-seq human written 4.6 years ago by RafaelMP110 • updated 4.6 years ago by Istvan Albert ♦♦ 80k
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Comment: C: Error with bowtie2
... I believe you have files with different numbers of reads. You should check this and verify the existence of singletons. ...
written 4.8 years ago by RafaelMP110
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Answer: A: Picard Exception: Illegal Mate State
... I worked with a pipeline of SNP analysis with GATK, bwa and Picard. When I ran "MarkDuplicates.jar" I found a similar error. I tried to fix with Samtools and others commands but did not work.    I needed to do another alignment compatible with Picard. I eliminated the error when I did: bwa mem -M ...
written 4.8 years ago by RafaelMP110
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Answer: A: I need to download a list of all human genes with their respective Esemble gene
... Introduction to BioMart Mining data Data Mining in Ensembl   ...
written 4.8 years ago by RafaelMP110
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Comment: C: I need to download a list of all human genes with their respective Esemble gene
... Hi! Do you tried Biomart? ...
written 4.8 years ago by RafaelMP110
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Answer: A: Create smaller bam file based on the list of sequences
... awk '$3 != "*"' file.sam > newfile.sam ...
written 4.8 years ago by RafaelMP110
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Trimming fastq with quality
... Hello everyone! I'm a newbie in analyzes with RNA-Seq. I have paired-end reads data (Sanger / Illumina 1.9) and would like to cut the reads using quality score. We have visualized data with FastQC and we tested the softwares: sickle, Spade, fastq quality filter (fastx) and AllPaths. The best result ...
fastq fastx rna-seq trim fastqc written 4.9 years ago by RafaelMP110 • updated 3 months ago by genomax68k

Latest awards to RafaelMP

Supporter 7 months ago, voted at least 25 times.
Epic Question 9 months ago, created a question with more than 10,000 views. For Trimming fastq with quality
Popular Question 14 months ago, created a question with more than 1,000 views. For Functional Genes x Pseudogenes
Popular Question 14 months ago, created a question with more than 1,000 views. For Functional Genes x Pseudogenes
Great Question 3.8 years ago, created a question with more than 5,000 views. For Trimming fastq with quality
Student 3.8 years ago, asked a question with at least 3 up-votes. For Trimming fastq with quality
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Trimming fastq with quality
Autobiographer 4.8 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 4.8 years ago, created an answer that has been accepted. For A: I need to download a list of all human genes with their respective Esemble gene
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: I need to download a list of all human genes with their respective Esemble gene

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