User: Dataminer

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Dataminer2.6k
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Posts by Dataminer

<prev • 318 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 3 months ago by Dataminer2.6k • updated 7 weeks 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 4 months ago by Dataminer2.6k
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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 4 months ago by Dataminer2.6k • updated 20 days ago by mc25480
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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 5 months ago by Dataminer2.6k
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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 5 months ago by Dataminer2.6k
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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 5 months ago by Dataminer2.6k
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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 5 months ago by Dataminer2.6k • updated 5 months ago by Gautier Richard280
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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 6 months ago by Dataminer2.6k
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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 12 months ago by Dataminer2.6k
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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 12 months ago by Dataminer2.6k

Latest awards to Dataminer

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