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User: Dataminer

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Dataminer • 2.7k
Reputation:
2,670
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Location:
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Last seen:
1 month ago
Joined:
9 years, 4 months ago
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Posts by Dataminer

<prev • 318 results • page 1 of 32 • next >
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Mismatch in probe ids
... Dear members, I am using "An end to end workflow for differential gene expression using Affymetrix microarrays" as described [here][1] at one of the step it requires to map probe ids to gene names and symbols. The methods uses anno_palmieri <- AnnotationDbi::select(hugene10sttranscriptcl ...
microarray affymetrix written 7 weeks ago by Dataminer • 2.7k • updated 7 weeks ago by Kevin Blighe ♦ 63k
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Comment: C: Processing bulk RNA-seq TMM matrix to get DEGs
... Thank you for your reply. I concur, that raw reads are more useful than these normalised read counts. I was hoping for a work around but it seems that there isn't any. ...
written 4 months ago by Dataminer • 2.7k
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Processing bulk RNA-seq TMM matrix to get DEGs
... Dear Community, I am using a publicly available RNA-seq datasets that were processed as follows: "Gene expression normalizations were performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene length. In addition, only the genes and t ...
rna-seq written 4 months ago by Dataminer • 2.7k • updated 4 months ago by ATpoint ♦ 36k
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Your favourite workflow for Hi-C data analysis (Plant Genome)
... Dear Community, A lot of tools are present for Hi-C data analysis, some these include HiCCUPs, diffHiC. Fit-HiC, mHiC, hicexplorer, HiPPIE etc. My question is regarding Hi-C data analysis associated with plant genomes. In plant genomes we encounter polyploidy and repeats. This also results in hand ...
hi-c written 16 months ago by Dataminer • 2.7k • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: Paired end peak callers
... Hi Fredrieke, Thank's for the Genrich. I am not after any specific functionality, in general I have found that MACS2 doesn't work quite well with H3K9me3 or H3K27me3 marks (might be more). I don't know what the issue is and how it can be fixed. On the other hand PeakRanger (CCAT) works quite well w ...
written 17 months ago by Dataminer • 2.7k
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Paired end peak callers
... Hi, Are their any peak callers other than macs that can be used for paired end data ? If yes, please describe your experience with them. Thank you ...
chip-seq written 17 months ago by Dataminer • 2.7k • updated 12 months ago by gable_works • 40
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Comment: C: Hi-C data alignment with star
... Hi, I was using exactly the same bwa mem -A1 -B4 -E50 -L0 -t 12 ref.fa file1.fastq Btw I have plant genome polyploidy ...
written 18 months ago by Dataminer • 2.7k
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Comment: C: Hi-C data alignment with star
... Definition: 5 days of processing on HPC, with 12 threads and 132 Gb RAM. I understand that Hi-C data is huge and will take time, however 5 days is a lot :) ...
written 18 months ago by Dataminer • 2.7k
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Comment: C: Hi-C data alignment with star
... Hi Santosh, This is working fine no error, I will have a look at the link, thank :) ...
written 18 months ago by Dataminer • 2.7k
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Hi-C data alignment with star
... Dear community, Does anyone has experience with aligning data using star aligner? It would be very kind of you to share the syntax that you used or have a look at mine and point corrections (chimeric reads alignments etc) As reads from both strands need to be mapped seperately, I am using followin ...
hi-c star written 18 months ago by Dataminer • 2.7k • updated 18 months ago by Gautier Richard • 280

Latest awards to Dataminer

Great Question 6 weeks ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Great Question 3 months ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Epic Question 3 months ago, created a question with more than 10,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 11 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Great Question 11 months ago, created a question with more than 5,000 views. For Conversion Form Broad Peak Format Of Macs2 To Narrow Peak Format
Prophet 11 months ago, created a post with more than 20 followers. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 11 months ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Great Question 15 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 16 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 18 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
Great Question 2.0 years ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to check if my SNPs are also present in 1000 genome project
Great Question 2.0 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 2.1 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 2.5 years ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Epic Question 2.5 years ago, created a question with more than 10,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 2.5 years ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
Great Question 2.5 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
Great Question 2.5 years ago, created a question with more than 5,000 views. For Chip Seq Data Analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
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