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User: juara

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juara • 30
Reputation:
30
Status:
New User
Location:
Canada
Last seen:
6 days, 21 hours ago
Joined:
5 years, 9 months ago
Email:
n**********@gmail.com

Posts by juara

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Does GSVA normalize sampleset?
... Hi again, so I found out that in the case of `method = "ssgsea`, there is a normalization step across samples and genesets. It can be turned off with `ssgsea.norm = FALSE` to get scores independent of samples and genesets. However, I still have the same normalization issue with `method = gsva`. Th ...
written 4 weeks ago by juara • 30
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Does GSVA normalize sampleset?
... Hello, I have a log2 normalized TPM dataset that I would like to do pathway enrichment analysis. I thought GSVA and ssGSEA would output enrichment scores independent of sample set. However, when I subset my dataset and rerun GSVA, I get totally different set of scores. Do you have an idea what that ...
ssgsea gsva rna-seq written 5 weeks ago by juara • 30 • updated 27 days ago by Elucidata • 120
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Extract cNMF cluster membership
... Hello all, my question is relevant to https://www.biostars.org/p/383688/ . I still do not understand how `consensusmap()` assigns each sample to a cluster as shown in consensus track. Manual plotting of maximum values from `coef(res)` gives me the basis component and not consensus cluster. Any com ...
nmf written 5 weeks ago by juara • 30
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Counts plot does not match fold change between groups
... Hello all, I have patient data that are grouped based on a characteristic. I ran DESeq2 between the two groups following the tutorial. Everything seems fine but when I plot one of the top differentially regulated genes using `plotCounts()`, it seems the difference is driven by few outliers. Here is ...
deseq2 rna-seq written 3 months ago by juara • 30 • updated 3 months ago by jordi.planells • 380
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Adjusting for batch effect and covariates with ComBat
... Dear All, my question is related to this post: https://www.biostars.org/p/275874/ I have a heterogeneous RNAseq dataset in TPMs from 66 samples and two sequencing batches (64 from one batch, 2 from the second batch). This dataset contains many disease types (categorical), sample types (categorical ...
combat rna-seq batch effect written 3 months ago by juara • 30
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Mutect2 t_depth not matching total reads
... Hello I have a rather naive question. I ran GATK4 mutect2 on my samples with the following flags: --contamination-fraction-to-filter 0.0 --max-reads-per-alignment-start 0 The former is to disable downsampling process. So, theoretically I should be able to have equal values in t_depth column (to ...
sequencing gatk next-gen snp mutect2 written 2.6 years ago by juara • 30
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Comment: C: VCF files-Keep all alternative alleles
... Thank you very much for your comment. this works like charm! :) I am just wondering, whether there is a function in bcftools that I can merge FORMAT field data to INFO field with? ...
written 2.6 years ago by juara • 30
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Comment: C: VCF files-Keep all alternative alleles
... Yes I tried that too. The bcftools comment works though! Thanks ...
written 2.6 years ago by juara • 30
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VCF files-Keep all alternative alleles
... Hello I have VCF outputs of Mutect2 (GATK4) with no downsampling. Some variants have multiple calls, which are comma separated in ALT column. I would like to preserve all of them before inputting in VEP including their respective TLOD and AF scores into a new VCF file where each alternative allele ...
vcf bcftools samtools vcftools snp written 2.6 years ago by juara • 30 • updated 2.6 years ago by Pierre Lindenbaum ♦ 134k
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Download slices of SRA/FastQ files?
... Hello I am interested in specific loci of the genome in TARGET WGS data and so am trying to download only those regions as opposed to the whole SRA files which takes forever to download. So far, I figured that I can download the SRA files, convert them to BAM, take a slice of interest and delete th ...
wgs next-gen data retrieval sequencing written 3.4 years ago by juara • 30

Latest awards to juara

Popular Question 2.6 years ago, created a question with more than 1,000 views. For TCGA data analysis, raw_count?!
Popular Question 2.6 years ago, created a question with more than 1,000 views. For TCGA exons data-de novo isoform assembly
Popular Question 2.6 years ago, created a question with more than 1,000 views. For PDB visualization methods
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Download slices of SRA/FastQ files?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For TCGA data analysis, raw_count?!
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