Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
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Joined:
6 years, 5 months ago
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Posts by Jean-Karim Heriche

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Comment: C: 3d reconstruction of confocal data
... This may not be the most appropriate place for this kind of question though I can't think of a place to redirect you. Anyway, it depends on what you mean by "model the 3d reconstruction". Software provided by most confocal microscope vendors should allow you to do basic reconstruction. Otherwise, a ...
written 6 hours ago by Jean-Karim Heriche13k
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Comment: C: How to build HMM from position weight matrix?
... No, you need emission and transition probabilities for a HMM. A PWM only encodes the probabilities of seeing each nucleotide for every position. What I am suggesting is to view the PWM as a HMM by considering the PWM as giving emission probabilities with transition probabilities set to 1. ...
written 2 days ago by Jean-Karim Heriche13k
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Comment: C: How to estimate the minimal amount of sequencing required for a biomarker analys
... Assuming the counts are Poisson-distributed with rate r, for r sufficiently large (> ~20, but the approximation is already quite good before this, it only improves as r increases), the Poisson distribution could be approximated by a Gaussian distribution with mean r and variance r. You could also ...
written 3 days ago by Jean-Karim Heriche13k
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Answer: A: Where I can download reference genomes of sequenced Norway spruce, Pine and Betu
... The conifer genome network website has [links to various conifer genome projects][1]. The university of Umeå hosts the [Norway spruce genome project][2], check their FTP site. [A scaffold assembly for Betula pendula][3] and [a pseudo-chromosome assembly][4] are available on the CoGe website. Betula ...
written 4 days ago by Jean-Karim Heriche13k
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Comment: C: perl script not giving output
... One thing to look for is that when reading from a file, the variable includes the end of line character(s), so in your case $rs_id contains the whole line including the \n character (assuming Linux), e.g. $rs_id contains 'rs1234\n'. So later when trying to match, you still have this end-of-line char ...
written 5 days ago by Jean-Karim Heriche13k
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Comment: C: How to know which is coding gene in GTF File
... Yes and no, it depends on what you're after. Genes labelled as protein-coding are those that are usually of interest but they are not the only ones producing polypeptides, for example some pseudogenes can produce proteins, the immunoglobulin genes are protein-coding genes. Pseudogenes generally have ...
written 5 days ago by Jean-Karim Heriche13k
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Comment: C: Parallelize consensusClusterPlus package
... Check you're not running out of memory on the server. ...
written 6 days ago by Jean-Karim Heriche13k
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Answer: A: How to know which is coding gene in GTF File
... Since you're using Ensembl, have a look at the [GENCODE/Ensembl list of gene/transcript biotypes][1]. [1]: https://www.gencodegenes.org/gencode_biotypes.html ...
written 6 days ago by Jean-Karim Heriche13k
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Comment: C: Statistical modelling - how to findout the significance of a sequence feature
... Looks like a school assignment. We're not going to do it for you. Show us what your reasoning is and where you're stuck and someone may help you. ...
written 6 days ago by Jean-Karim Heriche13k
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Comment: C: How to build HMM from position weight matrix?
... This doesn't look like a typical position weight matrix but rather a matrix of probabilities at each position. A position weight matrix corresponds to the log of the frequencies normalized to a background model. Anyway, you could view it has an HMM (the values represent emission probabilities) so co ...
written 8 days ago by Jean-Karim Heriche13k

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