User: i.sudbery
i.sudbery • 2.4k
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Posts by i.sudbery
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... I've not really used the ballgown pipeline beyond playing about with it. My own preferred pipeline is `salmon` -> `tximport` -> `DESeq2`, although I can see the conceptual advantages in using `sleuth`. If I want an experiment specific transcript annotaiton, I'll assemble that first with string ...
written 2 days ago by
i.sudbery • 2.4k
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... There are two main differences between the Kallisto-sleuth pipeline and the 'Ballgown' pipeline.
Sleuth makes use of Kallisto's bootstrap analyses in order to decompose variance into variance associated with between sample differences and variance associated with quantificaiton uncertainty. I don't ...
written 7 days ago by
i.sudbery • 2.4k
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... To add to what others have said, knowing a lot of these is probably not useful, but being able to *recognise* the common ones will probably be helpful (know what they are when you see them, but neccesarily be able to write them yourself). I doubt anyone "learnt" these deliberately, they just become ...
written 9 days ago by
i.sudbery • 2.4k
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... I don't know about file formats for protein arrays, but my guess is that the data is going to be similar in format to microarray data: a large number of florescence intensity readings in a spatially arrayed format. Thus you will probably be able to analyse the data with limma, although it will proba ...
written 16 days ago by
i.sudbery • 2.4k
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5
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Answer:
A: SRA to fastq
... Not quite an answer to the question you are asking, but the ENA (European Nucleotide Archive) has all publically available SRA samples for download directly as fastq. The download will take much longer (unless you use aspera), but the you more than make up for it in conversion time. ...
written 16 days ago by
i.sudbery • 2.4k
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... I always deposit in GEO (which automatically forwards to SRA/ENA). I've never had any stress with it. Its dull, yes (copying the same info across many boxes), but I can't say a dataset has ever taken me more than a few hours. ...
written 4 weeks ago by
i.sudbery • 2.4k
3
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113
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... GEO (US) or ArrayExpress (Europe), depending on preference. It doesn't really matter which because if you deposit in one, it will be automatically mirrored in the other. Also submission to either results in automatic submission of your data to SRA / ENA.
FAIRsharing is a database of databases, it ...
written 4 weeks ago by
i.sudbery • 2.4k
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... I think your problem is probably in this line here:
lengthData=median(width(txsByGene))
What you are doing here is getting the length of the primary transcript: i.e. the distance from the TSS to the TTS. Actually what you need is the sum of the exon lengths (i.e. excluding the introns). You ca ...
written 5 weeks ago by
i.sudbery • 2.4k
2
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... There are many reviews on this subject of find lncRNAs.
Try this [one][1] and this [one][2] for starters.
Both of these concentrate on species where the genome is available, but have some useful tips if you are looking to put together a protocol for doing in an unannotated genome.
I guess you' ...
written 5 weeks ago by
i.sudbery • 2.4k
1
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... I personally like EBI's [Expression Atlas][1],but I don't think the eye is one of their tissues. In fact I'm not aware of any expression atlas that includes the eye (not saying it doesn't exist).
[1]: https://www.ebi.ac.uk/gxa/home ...
written 5 weeks ago by
i.sudbery • 2.4k
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