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User: Dataminer

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Dataminer • 2.6k
Reputation:
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Location:
Netherlands
Last seen:
2 days, 18 hours ago
Joined:
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Posts by Dataminer

<prev • 315 results • page 1 of 32 • next >
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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 27 days 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 27 days 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 27 days 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 27 days ago by Dataminer • 2.6k • updated 27 days ago by Gautier Richard • 230
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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 weeks 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 8 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 8 months ago by Dataminer • 2.6k
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Comment: C: BigWig from ensembl assembly to UCSC session
... Could you suggest something. I don't want to realign as it will cost a lot of time and the other option is to generate wiggle track (add chr)and convert them into bigwigs. But is it possible to add "chr" to the existing bigwigs and make them work? ...
written 8 months ago by Dataminer • 2.6k
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Comment: C: BigWig from ensembl assembly to UCSC session
... I know how to fix this in wiggle files but I have no clue how to fix this in bigwigs. ...
written 8 months ago by Dataminer • 2.6k
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Comment: C: BigWig from ensembl assembly to UCSC session
... Reviewer wants UCSC session and I don't want to realign the data. ...
written 8 months ago by Dataminer • 2.6k

Latest awards to Dataminer

Student 7 days ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
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Popular Question 6 months 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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Popular Question 12 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 12 months ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Epic Question 12 months ago, created a question with more than 10,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 12 months ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
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Great Question 12 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Popular Question 12 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 12 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 19 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Extracting List Of Genes Associated With A Pathway In Kegg
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Popular Question 19 months ago, created a question with more than 1,000 views. For Database For Genes Implicated In Lymphoid And Myeloid Development
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Popular Question 19 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 19 months ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
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