Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Comment: C: Optimize bwa mem in parallel on a SLURM cluster
... Indeed my bad. copy/paste error. I solved it now ...
written 4 days ago by Nicolas Rosewick6.6k
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Comment: C: Optimize bwa mem in parallel on a SLURM cluster
... $SLURM_ARRAY_TASK_ID is a variable that report the job array ID. check here for information concerning job arrays : https://slurm.schedmd.com/job_array.html . ...
written 4 days ago by Nicolas Rosewick6.6k
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Comment: C: discrepancy between reads
... Yes only one allele seems to have the deletion. The other not. ...
written 4 days ago by Nicolas Rosewick6.6k
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Comment: C: Optimize bwa mem in parallel on a SLURM cluster
... indeed 10GB is maybe too small. It was for the example ;) I added an example of sample sheet also. ...
written 4 days ago by Nicolas Rosewick6.6k
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Answer: A: Optimize bwa mem in parallel on a SLURM cluster
... One good idea is to use a job array that takes a samplesheet in input. Each line specifies one sample. Then using SLURM_ARRAY_TASK_ID variable in the slurm bash script you can acces the respective line in your sample sheet and execute a bwa mem instance with the number of CPU specified in the slurm ...
written 5 days ago by Nicolas Rosewick6.6k
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Comment: C: how to calculate Average of purchases of distinct items in the session using dpl
... Hello shameenkhan075! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. Better ask https://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. I ...
written 16 days ago by Nicolas Rosewick6.6k
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Comment: C: STAR alignment results in large chunks of NNNNNs
... As Devon explains it's a splicing. You can open your bam file in IGV and look at this read and you will see that it's spliced. ...
written 22 days ago by Nicolas Rosewick6.6k
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Comment: C: best way to visualize bam file
... What is the RAM of your computer ? What is the size of you bam file ? Which type of data ? If DNA-Seq (WGS, WES, ..) what will be the coverage, etc... ...
written 4 weeks ago by Nicolas Rosewick6.6k
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Answer: A: best way to visualize bam file
... You can direcly open your sorted and indexed bam file in IGV. It's not required to convert it to bedgraph. ...
written 4 weeks ago by Nicolas Rosewick6.6k
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Comment: C: Expression of specific genes between tumor and normal
... normalized read count should be ok. Best would be to plot the results as a boxplot for example. check DESeq2 vignette for more information : https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#differential-expression-analysis ...
written 9 weeks ago by Nicolas Rosewick6.6k

Latest awards to Nicolas Rosewick

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 3 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Popular Question 3 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 7 days ago, created a question with more than 5,000 views. For featureCounts exon counting problem
Popular Question 25 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 9 weeks ago, created a question with more than 5,000 views. For bigwig to peak
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Appreciated 11 weeks ago, created a post with more than 5 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 bigwig to peak
Student 3 months ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Epic Question 3 months ago, created a question with more than 10,000 views. For Download Rrna Sequences
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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Great Question 5 months ago, created a question with more than 5,000 views. For bigwig to peak
Popular Question 5 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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