Moderator: i.sudbery

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i.sudbery6.3k
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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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Comment: C: RNA seq and Invitro data not matching
... I changed this answer because I miss-read the question and thought the "invitro" data and the RNAseq were going in opposite directions. ...
written 1 day ago by i.sudbery6.3k
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Answer: A: RNA seq and Invitro data not matching
... All experimental technique have a limit to their precision. Thus, the estimated foldchange we get out of both qPCR and RNAseq is just that - an estimate. That is why we put error bars on things - the error bars (at least if they represent the 95% confidence interval, which they normally should) mo ...
written 2 days ago by i.sudbery6.3k
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Rename Tag in BAM file
... Lets say I have a BAM file with a read like so: SRR2057595.3333414_ATCGG 0 chr19 3571763 255 44M * 0 0 * * XA:i:2 MD:Z:13C27C2 NM:i:2 BX:Z:ATCGG but a program I want to use requires what is currently in the `BX` tag to be in the `UM` ...
bam written 3 days ago by i.sudbery6.3k • updated 3 days ago by Pierre Lindenbaum124k
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Comment: C: db-GaP / GTEx analysis on the cloud. Easiest way?
... I'm not so sure how "cool" it is. NCBI just added $15,000 to the cost of my research project. ...
written 6 days ago by i.sudbery6.3k
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Answer: A: db-GaP / GTEx analysis on the cloud. Easiest way?
... The NCBI would like you to use the [AnVIL][1] service, which is hosted on the Google Cloud (US region). The data itself is stored in a US region Google Cloud Bucket. Using it within US region GC is free, but data egress outside google or to another google region incurs a charge. About 8 cents a GB ...
written 6 days ago by i.sudbery6.3k
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Comment: C: Effect of gene size on WGCNA
... Just published, this paper seems relevant: https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000481&type=printable They find that: a) Gene length bias goes beyond just longer genes have more reds, and finds that there are sample-specific length bias' b) That there are ...
written 7 days ago by i.sudbery6.3k
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Answer: A: is there any database that show RNA false positive?
... One obvious thing to try is to cross check against a database of known RNA-editing sites like [REDIportal][1]. However, such databases are envitably incomplete. I'd be extra cautious about any A:G change that is supported only by RNAseq. You could also check if your gene has any pseduogenised copi ...
written 11 days ago by i.sudbery6.3k
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Comment: C: What aligners to choose between Hisat2 and BWA for chip-SEQ analysis
... Used with a standard genome index (like I think most people do), there is no advantage to HiSat2 over BWA for ChIP-seq. You'll probably find that BWA is faster. However, it is possible to build Hisat2 indicies to be aware of variant positions in the genome and so map reads even if they contain the ...
written 12 days ago by i.sudbery6.3k
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Answer: A: relevance of GSEA on Nanostring ncounter gene expression data ?
... Yes, used naievely it would be biased. However, you should be able to set your "background" set to only include the 700 genes, not all genes in the genome. To show this, I appeal to a slight simpler situation - standard hypergeometric enrichment analysis (i.e GO analysis). For example if 20% of my ...
written 12 days ago by i.sudbery6.3k
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Comment: C: Effect of gene size on WGCNA
... I should point that normalising by gene length wouldn't change any of this. ...
written 13 days ago by i.sudbery6.3k

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Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 11 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 13 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 19 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 19 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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Scholar 23 days 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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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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