User: Dataminer
Dataminer • 2.5k
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Posts by Dataminer
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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 6 days ago by
Dataminer • 2.5k
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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 5 months ago by
Dataminer • 2.5k
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... I can try but not sure if these guys will accept it. ...
written 5 months ago by
Dataminer • 2.5k
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... 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 5 months ago by
Dataminer • 2.5k
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... I know how to fix this in wiggle files but I have no clue how to fix this in bigwigs. ...
written 5 months ago by
Dataminer • 2.5k
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... Reviewer wants UCSC session and I don't want to realign the data. ...
written 5 months ago by
Dataminer • 2.5k
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... Dear Community,
I am having trouble in viewing my data in UCSC and I am not sure what is going wrong.
Situation#: I have my bam files aligned using ensembl assembly and then preprocessed and generated bigwigs (deep tools) and then uploaded at UCSC (no errors). But as soon as I visualise the track ...
written 5 months ago by
Dataminer • 2.5k
• updated
5 months ago by
Devon Ryan ♦ 86k
1
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Comment:
C: heat map and Survival plot
... Thank's a lot. Very helpful. ...
written 6 months ago by
Dataminer • 2.5k
0
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304
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Comment:
C: heat map and Survival plot
... These are all female samples and I don't have the normals. What I can think of that the median expression can be made used in deceased and living(may be). ...
written 6 months ago by
Dataminer • 2.5k
0
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1
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304
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Comment:
C: heat map and Survival plot
... This is all I have got. May be OS can be used, I am very new to this kind of analysis.
...
written 6 months ago by
Dataminer • 2.5k
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