Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Comment: C: Supporting a tool written in R
... Hello kuckunniwid! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. Better ask on stackoverflow.com For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you dis ...
written 5 hours ago by Nicolas Rosewick8.3k
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Comment: C: Run R script on 100 files using for loop
... try `write.geno(wind, paste0(the_dir, basename(file)))` ...
written 1 day ago by Nicolas Rosewick8.3k
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Answer: C: Run R script on 100 files using for loop
... change `wind <- fread(fileNames)` to `wind <- fread(file)` and `output=geno2lfmm("file")` to `output=geno2lfmm(file)` ...
written 1 day ago by Nicolas Rosewick8.3k
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Comment: C: Fisher's exact test for Copy Number Variation association in R
... If you can translate your data in a contingency table then it's easy to perform a fisher exact test in R. ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: GATK quality recalibration to get recalibrated BAM files before SNP calling
... you don’t have access to an other cluster (your institution maybe has a bigger one ? ). One node with 28 cores is clearly not a lot to process 500 exomes.. however BQSR use only one core per sample. So you could in theory process 28 samples in parallel thus dropping the compute time for 300 samples ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: GATK quality recalibration to get recalibrated BAM files before SNP calling
... An exome file should run under a day for sure (in my case it takes 2-3 hours on my local cluster depending on the number of reads). Could you tell me more on the computational resource you have ? ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: GATK quality recalibration to get recalibrated BAM files before SNP calling
... Do you have a reason to use the spark version ? Did you try the “standard” version of BQSR ? ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: GATK quality recalibration to get recalibrated BAM files before SNP calling
... Could you post your command and gatk version ? ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: GATK quality recalibration to get recalibrated BAM files before SNP calling
... @rohitsatyam102 It’s --bqsr-recal-file not --bqsr_recal_file ...
written 2 days ago by Nicolas Rosewick8.3k
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Comment: C: ways to improve SnpEff prediction
... how did you filter your vcf ? Did you use the same filters as the original paper ? ...
written 18 days ago by Nicolas Rosewick8.3k

Latest awards to Nicolas Rosewick

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 15 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 17 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 21 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
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Student 6 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
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 9 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
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 3 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
Scholar 4 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Student 4 months ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
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
Scholar 4 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 4 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
Popular Question 5 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz

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