Moderator: Nicolas Rosewick

gravatar for Nicolas Rosewick
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Posts by Nicolas Rosewick

<prev • 1,002 results • page 1 of 101 • next >
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Comment: C: feature selection using random forest
... which type of data : RNA-Seq, microarray ? ...
written 12 hours ago by Nicolas Rosewick8.6k
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Comment: C: Cutdapt for batch processing ?
... what did you try ? start maybe by a combination of `ls` and `xargs` ? ...
written 1 day ago by Nicolas Rosewick8.6k
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Answer: A: How to determine the list of all genes (at least expressed once in RNA Seq Exper
... I guess GTEx can help you : https://gtexportal.org/home/ ...
written 5 days ago by Nicolas Rosewick8.6k
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Comment: C: GSVA on RNAseq data (GTEX)
... Hi @Kevin. Is there a reason you used the rlog transformation (with kcdf="Gaussian") over the normalized count (with kcdf="Poisson") ? ...
written 7 days ago by Nicolas Rosewick8.6k
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Comment: C: Scatter / Gather for BaseRecalibrator on a single human WES dataset?
... Could you post your BQSR command please ? How many samples do you have ? BQSR should not take too much time in my experience.. ...
written 14 days ago by Nicolas Rosewick8.6k
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Comment: C: Should I keep up with random contigs in human genome
... Hi Wouter. In your knowledge do you know some paper discussing/benchmarking the impact of using hg38 (or hg19) with/without unplaced and unlocalized sequences on variant calling ? ...
written 29 days ago by Nicolas Rosewick8.6k
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Comment: C: Remove duplicate reads before variant calling?
... define "very large fastq file". IMO it's not a good idea to remove duplicate reads before alignment. You should mark duplicate reads (e.g. using picard markduplicates) on the aligned file (bam) and then call variants with the "markduplicated" bam file. ...
written 5 weeks ago by Nicolas Rosewick8.6k
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Comment: C: Should I merge the Paired-end RNA-seq reads for BLAT for intron identification
... STAR handles well non-canonical splice sites. If you want to reduce penalty of non-canonical splice sites by changing `--scoreGapNoncan` to -4 or even 0 (default is -8). You may also change `--scoreGapGCAG` and `--scoreGapATAC` to 0. Be aware that you may increase false positive splice-reads. I sugg ...
written 5 weeks ago by Nicolas Rosewick8.6k
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Answer: A: Should I merge the Paired-end RNA-seq reads for BLAT
... You should use an aligner designed to align sequencing paired-end reads. BLAT was not designed to handle such data. Possible options depending on your organism : 1. If assembled genome is good and an annotation exists : - option A : - Align with STAR (use 2-pass option) - Count reads ...
written 5 weeks ago by Nicolas Rosewick8.6k
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Comment: C: Homozygot genotype information but SNP is heterozygous
... Here looking at DP, DPA and DPB you have 317 reads out ouf 317 with allele B thus homozygote. Did you check the bam file in IGV ? ...
written 8 weeks ago by Nicolas Rosewick8.6k

Latest awards to Nicolas Rosewick

Popular Question 3 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Appreciated 15 days ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 17 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 27 days ago, created a question with more than 5,000 views. For Cutadapt Or Fastx Clipper
Oracle 5 weeks ago, created more than 1,000 posts (questions + answers + comments).
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?
Student 7 weeks ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Epic Question 10 weeks ago, created a question with more than 10,000 views. For bigwig to peak
Student 11 weeks ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Appreciated 3 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
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
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
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 5 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 6 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz

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