Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Answer: A: tabix on 1000genome files
... 1000G chromosomes are encoded without "chr" as prefix. Try with `16:16000000-18000000` Also you can directly use tabix on the ftp stored files as : tabix ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 16:160 ...
written 24 days ago by Nicolas Rosewick8.8k
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Comment: C: How to create MAplot in R for only one sample?
... MAplot represents the average expression vs foldchange. Thus minium two samples are required to plot it. ...
written 27 days ago by Nicolas Rosewick8.8k
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Comment: C: Multiple hypothesis testing
... could you define the nature of the gene expression values (raw reads, TPM, fpkm, z-score, etc..). Also what did you already try ? ...
written 4 weeks ago by Nicolas Rosewick8.8k
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Answer: A: RNA seq data analysis and building co expression network
... Section 4 : https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html > **Can WGCNA be used to analyze RNA-Seq data?** Yes. As far as WGCNA is > concerned, working with (properly normalized) RNA-seq data isn't > really any different from working with (properly nor ...
written 4 weeks ago by Nicolas Rosewick8.8k
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Comment: C: PCA: log transform and scale=T/F?
... depends on your input data. Could you describe your input dataset please ? ...
written 4 weeks ago by Nicolas Rosewick8.8k
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Answer: A: Getting the db SNP VCF file for GRCh38.p13
... You can find it on GATK bundle : ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/ more information : https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle ...
written 5 weeks ago by Nicolas Rosewick8.8k
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Comment: C: gnoMAD mutation and essential gene
... what do you mean by "essential and non essential gene estimation" ? Please rephrase your question to provide more information. ...
written 7 weeks ago by Nicolas Rosewick8.8k
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How to force GATK haplotypecaller to output all genomic position (even non variant positions)
... Hi, Is there a way to force GATK haplotypecaller to output all genomic positions in the vcf; not only variant ones ? Example here : Top : Raw bam file Middle : -outbam using : `gatk HaplotypeCaller -R $genome -O test.vcf -I in.bam -ERC GVCF --max-alternate-alleles 3 -bamout test.bam -L interva ...
haplotypecaller gatk written 9 weeks ago by Nicolas Rosewick8.8k • updated 9 weeks ago by curious320
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Comment: C: how to find candidate genes using linear regression in R
... you can find p-values by using `summary` function in R : s <- `summary(lm(volatile~TPM[gene,]))` . p-values are stored in the `coefficients` component e.g. `s$coefficients` ...
written 9 weeks ago by Nicolas Rosewick8.8k
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Comment: C: Structural variation germline vs somatic ?
... do you have paired normal-tumor samples ? ...
written 3 months ago by Nicolas Rosewick8.8k

Latest awards to Nicolas Rosewick

Popular Question 7 days ago, created a question with more than 1,000 views. For Gviz : fill and line arrow color issues
Popular Question 7 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Epic Question 7 days ago, created a question with more than 10,000 views. For bigwig to peak
Popular Question 16 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Student 5 weeks ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 7 weeks ago, created a question with more than 5,000 views. For Cutadapt Or Fastx Clipper
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 3 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 4 months ago, created a question with more than 5,000 views. For Cutadapt Or Fastx Clipper
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Appreciated 5 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 5 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 5 months ago, created a question with more than 5,000 views. For Cutadapt Or Fastx Clipper
Oracle 5 months ago, created more than 1,000 posts (questions + answers + comments).
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?
Student 6 months ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Epic Question 7 months ago, created a question with more than 10,000 views. For bigwig to peak

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