Moderator: i.sudbery
i.sudbery ♦ 6.9k
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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
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... 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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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...
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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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... 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.sudbery ♦ 6.9k
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