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User: Dataminer

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Dataminer • 2.6k
Reputation:
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Netherlands
Last seen:
1 month, 3 weeks ago
Joined:
8 years, 7 months ago
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Posts by Dataminer

<prev • 315 results • page 1 of 32 • next >
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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 7 months ago by Dataminer • 2.6k • updated 5 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 8 months ago by Dataminer • 2.6k
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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 8 months ago by Dataminer • 2.6k • updated 12 weeks ago by gable_works • 20
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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 9 months ago by Dataminer • 2.6k
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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 9 months ago by Dataminer • 2.6k
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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 9 months ago by Dataminer • 2.6k
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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 9 months ago by Dataminer • 2.6k • updated 9 months ago by Gautier Richard • 280
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creating loom files using loomR
... Hi All, Has anyone here created a loom file using loomR package in R. The single cell RNA seq (10x) experiment files were processed using STAR and I have following files: 1. barcode.tsv AAACCTGAGAACTCGG-1 AAACCTGAGTAGGCCA-1 AAACCTGGTCGAAAGC-1 AAACCTGTCCTTAATC-1 AAACCTGTCGC ...
loomr rna-seq written 10 months ago by Dataminer • 2.6k
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Comment: C: BigWig from ensembl assembly to UCSC session
... Hey Devon, Thank you for your message. I have taken this file from `GRCh37_ensembl2UCSC.tx`t the link. I am doing this in terminal `python convertBigWigChroms.py GRCh37_ensembl2UCSC.txt Sort.Ref.ER.DSG.bam.bw ER.DSG.bw` and I get this error: Traceback (most recent call last): File "con ...
written 16 months ago by Dataminer • 2.6k
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Comment: C: BigWig from ensembl assembly to UCSC session
... I can try but not sure if these guys will accept it. ...
written 16 months ago by Dataminer • 2.6k

Latest awards to Dataminer

Great Question 5 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 6 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 8 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 15 months ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Popular Question 15 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 15 months 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 15 months ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
Popular Question 15 months 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 15 months ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Epic Question 20 months ago, created a question with more than 10,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 20 months ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 20 months ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
Great Question 20 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 20 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 20 months 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 20 months ago, created a question with more than 5,000 views. For Chip Seq Data Analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 20 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 2.3 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
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 2.3 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 2.3 years ago, created a question with more than 5,000 views. For Chip Seq Data Analysis
Great Question 2.3 years ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
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