User: i.sudbery
i.sudbery • 2.7k
- Reputation:
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- Sheffield, UK
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- IanSudbery
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- 2 days, 12 hours ago
- Joined:
- 3 years, 8 months ago
- Email:
- i********@sheffield.ac.uk
Posts by i.sudbery
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Comment:
C: limitations of Edge R or DEseq
... " to see DE among large number of samples". Sounds like you have replicates to me. See my answer here: https://www.biostars.org/p/292316/#292418 ...
written 6 days ago by
i.sudbery • 2.7k
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85
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... % reads unmapped: Too short is what you get when your read just don't map: If a read doesn't map, STAR will clip bases off the end of the read until either the read maps, or it is too short. So STAR is just saying that it can't map the reads. We recently had a similar problem where STAR wouldn't map ...
written 7 days ago by
i.sudbery • 2.7k
1
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99
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... I know of no tool that can do does this, and there are probably good reasons for that.
In the case of most protocols that use UMIs, **the UMI alone simply isn't unique enough to uniquely identify a pre-PCR molecule**. Consider: For deduplicating only on a UMI to work, it has to be far more likley ...
written 22 days ago by
i.sudbery • 2.7k
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4
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599
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4
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... transcript_tpm is the name of the dataframe, not a column in it. ...
written 23 days ago by
i.sudbery • 2.7k
1
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2
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157
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... and 58,000 is about right for the full gene set including non-coding. ...
written 29 days ago by
i.sudbery • 2.7k
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3.1k
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... Its a good point, but as far as I'm aware the only mapper that uses information from one read to inform the mapping of others is STAR in 2-pass mode. I'm pretty sure tophat doesn't. ...
written 4 weeks ago by
i.sudbery • 2.7k
1
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2
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721
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... Yes. Don't do short read single-end ChIP-seq. ...
written 4 weeks ago by
i.sudbery • 2.7k
0
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3
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237
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3
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Comment:
C: Fold change - a final explanation
... Well, that depends on the program. None of the standard rnaseq programs report regularized logs as default I don't think, other than DESeq, and even then it outputs the non-shrunk values as well. ...
written 4 weeks ago by
i.sudbery • 2.7k
5
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3
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237
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... There is what appears to be an error in your definition of fold change (could be an error, could be causal wording):
* A fold change describes the **ratio** of two values (not the difference). i.e. (expression condition 1)/(expression condition 2)
* The log2 fold changes are the log-of-the-fold-c ...
written 4 weeks ago by
i.sudbery • 2.7k
0
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10
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13k
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... Most stuff we do is done on a linux HPC that runs CentOS. People access this in different ways, but my preffered set up is a big windows box (Xeon, 32GB RAM) running a Xubuntu VM (which gets 20GB of that RAM).
I have SSHFS pipes set up to the disk areas on the HPC that allows me edit code in local ...
written 4 weeks ago by
i.sudbery • 2.7k
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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For A: Filtering during RNA Seq analysis?
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For C: if I am right about miRNA DE workflow
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For List of replication dependent and independent histone genes
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For A: Filtering during RNA Seq analysis?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher
4 weeks ago,
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For A: Filtering during RNA Seq analysis?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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9 weeks ago,
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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For A: Filtering during RNA Seq analysis?
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For C: if I am right about miRNA DE workflow
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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For UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
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For A: Filtering during RNA Seq analysis?
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For A: Alternative to Cufflinks ?
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