User: JJ

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JJ430
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430
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Posts by JJ

<prev • 149 results • page 1 of 15 • next >
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... will do - thanks so much! ...
written 14 days ago by JJ430
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... thanks so much for this pointer! ...
written 14 days ago by JJ430
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Pathway analysis with co-variates for RNA-seq data
... Hi all, I was wondering if someone knows of a tool to perform a pathway analysis with co-variates for RNA-seq data. What I mean in more detail is the following: I have two groups (cond. 1 vs. cond. 2) but I also have co-variates which will have an high impact on the expression (20-30 samples in t ...
rna-seq written 14 days ago by JJ430 • updated 14 days ago by Kevin Blighe39k
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Help with Designing an Approach for Biomarker Signature Generation
... Hi all, I am trying to design an experiment and could use some input. My goal is to generate a predictive gene signature, which can separate two groups BUT I have a number of confounding variables. My starting point are RNA-seq experiments. - compute gene expression from RNA-seq experiments (low ...
gene rna-seq written 16 days ago by JJ430
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Comment: C: SRA and the relationship between biosamples, experiments and runs
... Hi, thank you for taking another look! they are technical according to the [paper][1]. Thanks!!! [1]: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126911 ...
written 4 weeks ago by JJ430
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Comment: C: SRA and the relationship between biosamples, experiments and runs
... Thank you very much for your answer. However, I am still not getting it. Sorry ... I am trying to rap my head around it! > then before sequencing, the samples were prepared using 4 indexes, > that means the library preparation was done individually, generating > the 8 experiments. There ...
written 4 weeks ago by JJ430
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SRA and the relationship between biosamples, experiments and runs
... Dear all, Obviously I've read this (https://www.ddbj.nig.ac.jp/faq/en/biosample-bioproject-sra-e.html): > What is the relationship between BioSamples, SRA Experiments, SRA > Runs, and my data files? > > BioSample is descriptive information about > the biological source materials, ...
sequencing written 4 weeks ago by JJ430 • updated 4 weeks ago by JC7.6k
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Comment: C: Calculation of VAF (variant allele frequency)
... Thank you so much for your detailed answer! Now it's clear to me what the difference between MAF and VAF is and I am looking into the variant allele fraction and not MAF. I have a couple of cancer samples (actually cancer cell lines) and I want to look at the heterogeneity within each sample. I exp ...
written 6 weeks ago by JJ430
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Comment: C: Error using Tabix
... Why don't you index them quickly by yourself - this is very simple: tabix -p vcf ...
written 6 weeks ago by JJ430
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Calculation of VAF (variant allele frequency)
... Hi all, So, I am interested in computing the VAF (variant allele frequency) by extracting values from a VCF file. From my understanding, the VAF is calculated as follows: AD(second entry)/DP so e.g. AD = 8,4 DP = 12 VAF = 4/12 AD = 5,10 DP = 15 VAF = 10/15 Is thi ...
sequencing written 6 weeks ago by JJ430 • updated 6 weeks ago by Pablo Marin-Garcia1.8k

Latest awards to JJ

Popular Question 3 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Student 5 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Popular Question 6 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 6 months ago, created a question with more than 1,000 views. For Clustering data - data transformation (log2) highly improves clustering but why?
Voter 7 months ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 10 months ago, created 100 posts.
Student 10 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 10 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 16 months ago, voted at least 25 times.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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