User: CuriusScientist

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50
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Institute for Cancer Research, Dept. of Tumor Biology, Oslo University Hospital, Oslo, Norway
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https://www.linkedin.c...
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CuriusScientist
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3 days, 1 hour ago
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5 years ago
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Posts by CuriusScientist

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Extracting regions from .bam file using a .gff or .gtf file
... As I can see from [https://bedtools.readthedocs.io/en/latest/content/general-usage.html][1] BED6: A BED file where each feature is described by chrom, start, end, name, score, and strand. For example: chr1 11873 14409 uc001aaa.3 0 + and format of Ensembl gtf file is 1 havana gene 11869 14409 . ...
written 5 weeks ago by CuriusScientist50
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Comment: C: Different results from featureCounts using gene_id and gene_biotype
... makes sense. is there a way to work around this situation using featureCounts? the only way I can think of is using the following code library(Biostrings) library(biomaRt) ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl") my.genes <- rownames(GeneCounts) ...
written 6 months ago by CuriusScientist50 • updated 6 months ago by i.sudbery8.1k
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Different results from featureCounts using gene_id and gene_biotype
... Dear Community, I have been running featureCounts to count mapped reads in RNA-Seq paired-end data with the following parameters featureCounts -T 10 -t exon -s 2 -p -g gene_id -a -o mapped.bam I also desired to find the biotype associated so I ran featureCounts using the following command fe ...
biotype featurecounts subread rna-seq readcounts written 6 months ago by CuriusScientist50 • updated 6 months ago by i.sudbery8.1k
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featureCounts parameters for RNA-Seq
... Dear Community, I have been running featureCounts to count mapped reads in RNA-Seq paired-end data with the following parameters featureCounts -T 10 -t exon -s 2 -p -g gene_id -a -o mapped.bam as mentioned in http://bioinf.wehi.edu.au/featureCounts/ However, I came across two posts where ...
featurecounts subread rna-seq readcounts written 6 months ago by CuriusScientist50 • updated 6 months ago by h.mon30k
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Low-coverage whole-genome sequencing (LC-WGS) or ultra low-pass WGS analysis
... I am new to the genome analysis and want to analyse ultra low-pass WGS data for copy number variation analysis. It will be really helpful if the members of the community can check if the approach I have taken is correct # fetch information for read groups header=$(zcat ${sample_name}_R1_00 ...
genome lc-wgs next-gen sequencing ichorcna written 9 months ago by CuriusScientist50 • updated 8 months ago by Biostar ♦♦ 20
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Answer: A: Finding Variable Genes in Seurat, scRNA-seq
... > I found that changing x.low.cutoff between 0.0125 (in the PBMC 3k tutorial) and 0.1, for example, will have a huge effect on the number of variable genes > **@igor,** this is bound to happen as the number of genes is higher below 0 ( as can be seen by the dense plotting) I was facing the ...
written 18 months ago by CuriusScientist50
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cBioPortal genetic profile id and mutational data analysis
... Dear all, I recently started using cBioPortal and struggling to understand the terminologies used and what is the importance and application of a particular one over another and apologies for a long and naive question. The aim of my study is to understand the mutational profile. for the cancer st ...
gistic cna tcga cbioportal mutation assessor written 2.3 years ago by CuriusScientist50
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Comment: A: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... Many thanks to @igor for clarifying my doubts :) **how you think can I proceed with the following task** 1. I need to find the mutations in public databases 2. compare with in-house experimental results 3. perform analysis **Can I use the data/results from cBioPortal with those not part of cB ...
written 2.4 years ago by CuriusScientist50
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Comment: C: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... That clears some of my doubts ...
written 2.4 years ago by CuriusScientist50
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Comment: C: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... I can see that in the link mentioned by you cohort: GDC TCGA Prostate Cancer (PRAD) (11 datasets) and cohort: TCGA Prostate Cancer (PRAD) (22 datasets) what I want to know is how can I find what datasets are part of those 11 and 22 datasets? If I am not wrong some of them, if not all, must be par ...
written 2.4 years ago by CuriusScientist50

Latest awards to CuriusScientist

Student 3 months ago, asked a question with at least 3 up-votes. For DESeq2 model design: dose and time effect
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 model design: dose and time effect
Popular Question 4.3 years ago, created a question with more than 1,000 views. For DESeq2 model design: dose and time effect

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