User: ThePresident

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ThePresident60
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New User
Location:
Canada
Last seen:
7 years ago
Joined:
7 years, 6 months ago
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Posts by ThePresident

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Batch Clustering Of Genes According To Their Function Or Biological Process
... Sounds promising. I'll give it a try. Thank you. ...
written 7.1 years ago by ThePresident60
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Batch Clustering Of Genes According To Their Function Or Biological Process
... Hello, Quick question: I have a bunch of differentially regulated genes from bacterial RNA-seq experiment (test vs control). I would like to know if those DE genes present any kind of «enrichment» or clustering of particular processes (virulence, metabolic genes, transport and so on). Is there an a ...
written 7.1 years ago by ThePresident60 • updated 7.1 years ago by Sean Davis26k
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Comment: C: Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
... Honestly, yes. I don't know if others can confirms this, but I see it in my data. Of course, you have to log transform RPKM values otherwise the dispersion is enormous due to the extreme values. I've seen it also in at least one recent paper, but I just can't find the ref right now. ...
written 7.2 years ago by ThePresident60
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Answer: A: Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
... Could it be safe to trace a diagram of all RPKM values (should give a normal distribution), and then say that +/-1 sigma are "average/moderately" expressed genes, up of that are highly expressed genes and down are low expressed genes. Overall, you'll have 68.2% of average expression, and 15.9% of lo ...
written 7.2 years ago by ThePresident60
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Comment: C: Understanding Vcf Output From Mpileup
... "VDB checks if variant bases occur at random positions in the aligned portion of the reads" - couldn't be more clear along with that slides. Thanks! ...
written 7.2 years ago by ThePresident60
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Comment: C: Understanding Vcf Output From Mpileup
... Thank you for your answer. I already read samtools mpileup manual and the 1000 genomes, but the 2nd link was very useful. However, I still got some stuff to clear-up: First, since I'm working with a bacterial genome (so one single chromosome - one allele), I still don't catch what AC1=4 means? I wo ...
written 7.2 years ago by ThePresident60
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Answer: A: Estimating Error Rate In Sequencing Data
... I'm not sure to answer you question, but I know that you can use FastQC for estimation of the quality of one sequenced library. For exemple: curl -O http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip unzip fastqc_v0.10.1.zip cd FastQC chmod +x fastqc fastqc FileName.fastq ...
written 7.2 years ago by ThePresident60
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Answer: A: Rna Seq Data Analysis
... The file called "gene_exp.diff" will contain everything you need for differential expression (including statistical parameters). You might begin with that file to asses you DE genes. edit: you can use "genes.fpkm_tracking" to get your FPKM values which can be useful to compare genes expression wit ...
written 7.2 years ago by ThePresident60
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Understanding Vcf Output From Mpileup
... Hello, I asked this question at Seqanswers, but have not get any response yet. I have a question upon calling a SNPs from RNA-seq data (Illumina signle-read, bacterial) with mpileup. I got my VCF file and I'm struggling a little bit to understand the output. If I have: gi|xxx|emb|xxx| 143630 ...
snps mpileup written 7.2 years ago by ThePresident60 • updated 6.1 years ago by Biostar ♦♦ 20
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Comment: C: New Bioinformatics Courses At Cousera
... I'm new to Cousera, so just a quick question: I would like to sign up, but I'm not sure I'll be able to follow up everything including quizzes and all that... Is it possible or I'm better to wait to have full time? ...
written 7.2 years ago by ThePresident60

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