User: kennethcondon2007
kennethcondon2007 • 750
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Posts by kennethcondon2007
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... Can I just ask - how is the quality score increased? ...
written 18 hours ago by
kennethcondon2007 • 750
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... back ground reading:
https://www.biostars.org/p/101727/ ...
written 1 day ago by
kennethcondon2007 • 750
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... I believe spike-ins are used just to check that housekeeping genes are expressed in the correct proportions so are not appropriate for quantification.
TPM I believe is the most robust metric
As long as the samples come from the same experiment then they should be directly comparable because I woul ...
written 2 days ago by
kennethcondon2007 • 750
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... [Ensembl Biomart][1] allows you to download what you need.
First: select what is needed e.g. Dataset: Ensembl 89 + then choose species --> Filter: gene type --> lincRNA --> Attributes: Gene ID, Gene Name, Gene Type
Second: Click "results"
Third: Export all results to TSV --> Go
...
written 5 days ago by
kennethcondon2007 • 750
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... CPGplot actually plots occurance of CpG islands (the amount of times G is followed by C) not CG content (the total amount of G and the total amount of C independently)
Try FASTQC ...
written 5 days ago by
kennethcondon2007 • 750
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... Hi all,
I have developed a pipeline for predicting tissue specificity that currently includes expression data from 26 adult mouse tissues. I have been asked to find genes specific to pre-adipocytes. As undifferentiated cells, I am assuming that it would be a good idea to include their precursor - m ...
written 7 days ago by
kennethcondon2007 • 750
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... Any updates? I'm trying to find a reliable tool fr cross-species mapping. Unfortunately I can;'t find a bench mark on the tools that are out there. Suggestions welcome. ...
written 8 days ago by
kennethcondon2007 • 750
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... Any updates? I'm trying to find a reliable tool fr cross-species mapping. Unfortunately I can;'t find a bench mark on the tools that are out there. Suggestions welcome. ...
written 8 days ago by
kennethcondon2007 • 750
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... ranking = ordering
Order the file by significance (e.g. P-value, Q-value, or FDR) or change of expression (e.g. log fold change)
For example:
- Order a file of 1000 genes by q-value
- Gene x is first in the list because it has lowest p-value and is therefore rank 1
- Gene y is last in ...
written 8 days ago by
kennethcondon2007 • 750
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... You could extract the set of differentially expressed genes from the [gene_exp.diff][1] file and then use that list of genes as input in [gprofiler][2]
[1]: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-expression-tests
[2]: http://biit.cs.ut.ee/gprofiler/ ...
written 10 days ago by
kennethcondon2007 • 750
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