User: Dataminer
Dataminer • 2.7k
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Posts by Dataminer
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... 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 ...
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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 13 months ago by
Dataminer • 2.7k
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... 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 ...
written 13 months ago by
Dataminer • 2.7k
• updated
8 months ago by
gable_works • 40
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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 14 months ago by
Dataminer • 2.7k
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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 14 months ago by
Dataminer • 2.7k
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643
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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 14 months ago by
Dataminer • 2.7k
5
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... 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 ...
written 14 months ago by
Dataminer • 2.7k
• updated
14 months ago by
Gautier Richard • 280
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... 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 ...
written 16 months ago by
Dataminer • 2.7k
0
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758
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... 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 21 months ago by
Dataminer • 2.7k
0
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758
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... I can try but not sure if these guys will accept it. ...
written 21 months ago by
Dataminer • 2.7k
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