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Moderator: i.sudbery

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i.sudbery ♦ 9.4k
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Location:
Sheffield, UK
Twitter:
IanSudbery
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3 hours ago
Joined:
5 years, 7 months ago
Email:
i********@sheffield.ac.uk

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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Comment: C: How to deduplicate UMI with mapping shift ?
... So there IS an increase in the fraction of intersecting UMIs in the +1 and -1 positions. But that enrichment is also present in the null distribution, which is what suggests its an artifact driven by the fact that position super high coverage positions are likely to be close to other super-high cove ...
written 2 days ago by i.sudbery ♦ 9.4k
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... > it got rid of all the multimappers category, but instead of assigning them to multiple genes, as I would expect, they seem to all get moved into the Unassigned_Ambiguity category. Is there a reason it's doing this, or am I missing something? AFAIK `Unassigned_Ambiguity` means not that the rea ...
written 2 days ago by i.sudbery ♦ 9.4k
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Comment: C: miRNA target IDs to gene names
... I don't recognize that type of ID. What species is this? ...
written 4 days ago by i.sudbery ♦ 9.4k
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Comment: C: FDR for multiple contrasts
... In addition to this, you might check out stageR: https://bioconductor.org/packages/release/bioc/html/stageR.html I don't know if it can be adapted for protein data, but the idea is that you test for main effects first, and only test those interaction hypothesis for which the main effect is significa ...
written 4 days ago by i.sudbery ♦ 9.4k
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Comment: C: Way to check if gene A lies in the same ORF as gene B
... Which organism? What annotation? Are these ORFs on the same or different transcripts? ...
written 6 days ago by i.sudbery ♦ 9.4k
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Comment: C: Way to check if gene A lies in the same ORF as gene B
... Open reading frames are part of genes, not vice-versa. You cannot have two genes that are part of the same ORF. Do you mean how to check if the ORFs of two genes are in the same reading frame (i.e. 1, 2 or 3)? ...
written 6 days ago by i.sudbery ♦ 9.4k
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... So the short answer to this is no. As far as I'm aware, no one has written anything that can tell you what things your multi-mapping reads are mapping to. Really, the only way to do this is to look for high mapping rates to things that one would expect to generate multi-mappers (hence my suggestion ...
written 7 days ago by i.sudbery ♦ 9.4k
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Comment: C: Paper: Ten simple rules for biologists initiating a collaboration with computer
... Hard agree on that! If something is reproducible, it shouldn't matter which software you use to show it. I might not go as far as to say that what holds true with HiSat should hold true with Tophat (which is clearly documented to just not work as well). But what holds true with HiSat should hold tru ...
written 8 days ago by i.sudbery ♦ 9.4k
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Answer: A: Paper: Ten simple rules for biologists initiating a collaboration with computer
... I think it depends. I think it is probably quite a good guide for Bioinformaticians that want to collaborate with "proper" computer scientists when they need new computer science to solve their problems. I think its less good for biologists who need to collaborate with someone to give more computa ...
written 8 days ago by i.sudbery ♦ 9.4k
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... Try getting hold of a GTF file of repeat annotations, and quantifying against that. ...
written 8 days ago by i.sudbery ♦ 9.4k

Latest awards to i.sudbery

Appreciated 16 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 16 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 3 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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