User: kennethcondon2007

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Posts by kennethcondon2007

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Comment: C: changing quality score of the read
... Can I just ask - how is the quality score increased? ...
written 18 hours ago by kennethcondon2007750
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Comment: C: RNA-seq normalization methods for cross samples comparison?
... back ground reading: https://www.biostars.org/p/101727/ ...
written 1 day ago by kennethcondon2007750
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Comment: A: RNA-seq normalization methods for cross samples comparison?
... 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 kennethcondon2007750
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Comment: C: How to analyze differentially expressed lncRNA from total RNA
... [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 kennethcondon2007750
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Answer: A: Draw AT content plot across a DNA sequence
... 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 kennethcondon2007750
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Comparing expression of undifferentiated cells using ENCODE - which data sets?
... 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 ...
encode rna-seq written 7 days ago by kennethcondon2007750
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Comment: C: Translating Genomic Locations Between Species
... 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 kennethcondon2007750
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... 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 kennethcondon2007750
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Comment: C: Gene set enrichment analysis cuffdiff output
... 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 kennethcondon2007750
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Answer: A: Gene set enrichment analysis cuffdiff output
... 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 kennethcondon2007750

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