User: i.sudbery
i.sudbery • 1.5k
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- Sheffield, UK
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- IanSudbery
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Posts by i.sudbery
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... Take a look at an MDS plot of your data, is one of these replicates massively outlying? In any case it seems you need a stronger normalisation than you are doing. Hand-calculated TPMs generally use the total number of reads in a sample, but no mainstream RNAseq package uses this, in fact they exclud ...
written 13 days ago by
i.sudbery • 1.5k
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... Firstly 0.6 is not a good correlation.
Secondly, think about the normalisation you want:
* **if you are looking at changes between conditions** (and it appears you are because you are talking about genes which are up and genes which are down), you need to do between sample normalisation, but betw ...
written 14 days ago by
i.sudbery • 1.5k
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... Sorry, cf means "compared with" https://en.wikipedia.org/wiki/Cf. ...
written 26 days ago by
i.sudbery • 1.5k
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... You might like to try DaPars: http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html
Its the tool i've used the most, although its never led to any significant discovery for us. I'd be interested in how you get on cf roar. ...
written 27 days ago by
i.sudbery • 1.5k
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... The new version of [UMI-Tools][1] now has mechanisms for dealing with data that has inline cell barcodes.
[1]: https://github.com/CGATOxford/UMI-tools ...
written 28 days ago by
i.sudbery • 1.5k
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5 follow
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... We are proud to announce the release of UMI-Tools 0.5.
![enter image description here][1]
UMI-tools provides error aware tools for dealing with short random oligos (Unique Molecular Identifiers/Random Molecular Tags).
The novel, error corrected UMI deduplication algorithm was published [here][2]. ...
written 29 days ago by
i.sudbery • 1.5k
0
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3
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315
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... The solution is to use ENA rather than SRA - everything apart from the controlled access stuff is mirrored accross and ENA store the raw fastq, which can be downloaded directly by ascp. ...
written 7 weeks ago by
i.sudbery • 1.5k
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... My biggest problem with this is that for at least fastq data, the rate limiting step is generally the dump rather than the actual download. ...
written 7 weeks ago by
i.sudbery • 1.5k
1
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315
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... I once broke the universities connection to backbone when downloading many files simultaneously on unthrottled ascp. ...
written 7 weeks ago by
i.sudbery • 1.5k
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... To answer your actaul question... Its like this because this is what is actually stored in a BAM file, which are not quite just compressed SAM files. pysam acts as a wrapper around the htslib c library, which is the same thing samtools uses, and that returns a c-structure representing the read rathe ...
written 3 months ago by
i.sudbery • 1.5k
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