User: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Comment: C: Size of typical genomic data
... I took this information from https://www.biostars.org/p/47646/#47683 ...
written 5 days ago by Nicolas Rosewick6.3k
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Size of typical genomic data
... Hi, I'm preparing some slides and would like to have some uptodate information related to typical sizes of NGS applications (VCF and BAM) e.g. exome ; WGS ; RNA-Seq ; gene panels , etc... Looking in the litterature that's what I found (for 30x coverage and 2x100bp read length) Type of NGS ...
size genomic written 5 days ago by Nicolas Rosewick6.3k • updated 5 days ago by toralmanvar290
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Comment: C: Compute correlation for depth of coverage between 2 datasets with different leng
... I compute the mean value per genomic position. So you will end with two dataframes with the genomic position common to both original dataframes. Each position containing the mean of the DP values for this position. Thus not one value... ...
written 12 days ago by Nicolas Rosewick6.3k
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Comment: C: SAM CIGAR parsing and position counter in R
... What about insertion, deletion and splice junction encoded within CIGAR ? If I understand well you want to report all position where one read aligned. ...
written 13 days ago by Nicolas Rosewick6.3k
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Comment: C: SAM CIGAR parsing and position counter in R
... Just to be sure you want to extract from cigar the alignment length (so 25 in the first row). And add it to the start position. Could you rephrase your question please ? ...
written 13 days ago by Nicolas Rosewick6.3k
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes thanks I edited now. ...
written 13 days ago by Nicolas Rosewick6.3k
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes that's it. In this example I used the mean but I could also use max or median ...
written 13 days ago by Nicolas Rosewick6.3k
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... No it works for different number of homo and heterozygote genotyopes. `findOverlaps` only reports positions that are in both dataframes and filter out the others. ...
written 13 days ago by Nicolas Rosewick6.3k
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Answer: A: compute correlation for depth of coverage between 2 datasets with different leng
... As you have multiple value per each genomic position you might try to use the median or the mean per position. And then perfom the correlation. Here I will use the mean but you could use median or max depending on the question you want to answer. library(tidyverse) homozygotes.mean < ...
written 13 days ago by Nicolas Rosewick6.3k
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Answer: A: NGS analysis: how to handle paired-end reads
... Most of the modern tools for NGS (e.g. aligners) handle paired-end fastq.gz files. Just give them as input. For example bwa mem : bwa mem reference sample1_TTGCCTT_L008_R1_001.fastq.gz sample1_TTGCCTT_L008_R2_001.fastq.gz > alignment.sam ...
written 24 days ago by Nicolas Rosewick6.3k

Latest awards to Nicolas Rosewick

Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 13 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 24 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Great Question 6 weeks ago, created a question with more than 5,000 views. For bigwig to peak
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 10 weeks ago, created a question with more than 5,000 views. For Tophat: Compressed Fastq File (Gz)
Great Question 10 weeks ago, created a question with more than 5,000 views. For Tophat: Compressed Fastq File (Gz)
Popular Question 11 weeks ago, created a question with more than 1,000 views. For qRT-PCR analysis : average triplicates for statistical testing
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 3 months ago, created a question with more than 5,000 views. For Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 3 months ago, created a question with more than 5,000 views. For Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 4 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?

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