Moderator: i.sudbery
i.sudbery ♦ 5.0k
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- IanSudbery
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I am a Lecturer in Bioinformatics at the University of Sheffield, where my group studies all things gene regulation, but with a particular emphasis on post-transcriptional gene regulation and RNA-processing. I am also an author of the UMI-tools, iCLIPlib, CGAT and CGAT-core packages.
Posts by i.sudbery
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... Yes, it really is as simple as that as long as you expect your covariates to affect expression in a linear manner. ...
written 14 days ago by
i.sudbery ♦ 5.0k
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... Its always sensible to treat tSNE as a visualisation only tool, and not to use tSNE results for inference. My guess would be that if you are clustering and finding that your clustering algo treats something as one cluster, but it looks like two on your tSNE, that your clustering is right and the tSN ...
written 15 days ago by
i.sudbery ♦ 5.0k
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... WIthout knowing how these genomes were annotated its difficult to know. Indeed the answer may come down to doing your own orthology analysis.
Flybase has a list of orthology relationships for the species that it covers, which you can download here:
ftp://ftp.flybase.net/releases/FB2019_03/precomp ...
written 20 days ago by
i.sudbery ♦ 5.0k
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... Its not anything to do with the fact that you've said your GTF is in the folder `D:/ETMR_PNET_NORMAL_cuffdiff` and all the other files are in `D:/ETMR/ETMR_PNET_NORMAL_cuffdiff` is it? ...
written 22 days ago by
i.sudbery ♦ 5.0k
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... One thing you might want to deal with is reads that map equally well to both the maternal and paternal genomes. You probably want to exlcude these reads. One way to do that would be to create a diploid offspring genome using your phasing information, and then map to that, disallowing multi-mappers. ...
written 25 days ago by
i.sudbery ♦ 5.0k
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... It depends how the FDR is calculated. If you use the BH procedure, what you get is an estimate of the expected false discovery rate. Technically, the FDR is the smallest value that satisfied the inequality
E(Q) <= a*m0/m <= a
where Q is the FDR, a is the type I error rate we wish to cont ...
written 25 days ago by
i.sudbery ♦ 5.0k
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... The Coefficient of Variation is the ratio of the standard deviation to the mean (See Wikipedia).
Thus
M <- apply(eset_HTA20, 1, mean)
SD <- apply(eset_HTA20, 1, sd)
CV <- SD/M
I don't really understand what is going to in the code you quote, other than it looks like someone ...
written 25 days ago by
i.sudbery ♦ 5.0k
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... You can do this by first converting your sam file to a BAM file:
samtools view -bh samfile.sam > bamfile.bam
Now index the file:
samtools index bamfile.bam
And finall get the per reference counts:
samtools idxstats bamfile.bam
The first column will be the reference, and the thi ...
written 26 days ago by
i.sudbery ♦ 5.0k
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Comment:
C: Tabix on bed file can't parse
... That last error seems to suggest an unsorted file (although the name would suggest its sorted). What command did you use to sort the file?
It's unclear what is wrong with the first two errors, they look like perfectly good bed lines, but I can think of two possiblities:
1. The column delimiters a ...
written 26 days ago by
i.sudbery ♦ 5.0k
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... See for example:
https://support.bioconductor.org/p/97262/, which is a helpful post all round for this question. ...
written 26 days ago by
i.sudbery ♦ 5.0k
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