Moderator: i.sudbery

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i.sudbery6.9k
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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

<prev • 620 results • page 1 of 62 • next >
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Answer: A: Differential gene expression, starting from RSEM expected count values.
... Definately use tximport if you can. If I remember correctly, the `txi` object is a `list` with three slots: `$abundance` contains a matrix of TPMs, with one row per transcript and one column per sample, `$count` contains the same matrix for estimated counts, `$length` contains a vector with the le ...
written 3 hours ago by i.sudbery6.9k
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Comment: C: What's your preferred pathway enrichment analysis tool after DEG analysis and wh
... Indeed, most people use camera and cameraPR with t. But I think this would still suffer from length bias. You could use the [shrunken LFCs][1] that come out of DESeq2. However, there was recently [a paper][2] suggesting that even this still suffers from length bias. [1]: http://bioconductor.or ...
written 3 hours ago by i.sudbery6.9k
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Comment: C: umi_tools count omitting majority of reads
... When you `--ignore-umi` you will only keep one read per position. Because here your "positions" are genes, rather than co-ordinates, it will only keep one read per gene. Looking at the number of unique UMIs will help, but not completely solve your problem, because UMI-tools will collapse UMIs that ...
written 2 days ago by i.sudbery6.9k
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Answer: A: Transcriptomic data analysis
... You can't do transcriptomics data analysis by comparing FPKM values of genes between samples. Transcriptomic data require careful normalisation and specialised statistical tests. Any one of a number of packages are available to perform differential analysis of transcriptomic data. Please see vignet ...
written 2 days ago by i.sudbery6.9k
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Answer: A: Comparing RNA expression between different tissue type, but same Cancer.
... Sarcoma just means a cancer of non-connective tissue. So bone sarcoma and uterine sarcoma are not the same cancer. However.... If you have matched tumour and normal for each sample (that is, you have 12 bone normals and 28 Uterus normals), there is no statistical reason you can't compare both tissue ...
written 3 days ago by i.sudbery6.9k
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Comment: C: Can fusion transcript softwares distinguish between gene-fusions and transcript-
... All things are possible I guess. I know that you can get transcriptional read through and splicing of adjacent genes that have ended up on the same transcript, but this is the first I've heard of true intergentic-trans splicing. But I'd guess for any given transcript, the prior on whether something ...
written 7 days ago by i.sudbery6.9k
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Comment: C: Can fusion transcript softwares distinguish between gene-fusions and transcript-
... First do you know if your organism does transplicing or not? Most fusion transcript software is develop for use on cancer samples, and mammals don't do trans-splicing. If you are working in something that does do transplicing.... you could look at where the break point is? If its a transplice then ...
written 7 days ago by i.sudbery6.9k
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Comment: C: Unavailable 3' UTR regions of pig genes from Ensembl
... Hello yronjosephmanaig! Questions similar to yours can already be found at: Downloading 3' UTR sequences for miRNA Target Prediction We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply belo ...
written 8 days ago by i.sudbery6.9k
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Answer: A: Downloading 3' UTR sequences for miRNA Target Prediction
... For both of the genes you posted, the gene has multiple transcripts. Some of those transcripts have UTRs annotated, some don't. At least in these cases you shuold be able to find at least one transcript for the gene that has a UTR sequence. ...
written 8 days ago by i.sudbery6.9k
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Answer: A: Kruskal Wallis test with the same p-value for all data?
... You have only one data point in each group.You cannot do a kruskal wallis test with only one observation in each group. ...
written 9 days ago by i.sudbery6.9k

Latest awards to i.sudbery

Scholar 9 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
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 20 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 10 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 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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?
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?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 4 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Scholar 4 months ago, created an answer that has been accepted. For A: Is there any NGS tool which produce long pairwise reads?
Scholar 4 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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