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User: michealsmith

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michealsmith • 740
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Posts by michealsmith

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Comment: C: Deep learning for genetics model of polygenic complex disease.
... Many thanks. I just briefly read DeepWAS, it seems it first implement deep-learning-based DeepSEA to annotate functional SNP, then simply apply logistic regression to classify disease/control. This is good enough, but my question is looking for work that directly apply deep learning for classificati ...
written 19 months ago by michealsmith • 740
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Deep learning for genetics model of polygenic complex disease.
... We know in recent several years very quickly deep learning (We could see as advanced multi-layer neural network) has achieved success in picture recognition, which could revolutionize medical diagnosis for example neurological disease diagnosis based on fMRI data. I'm genetics person for complex d ...
deep learning disease genetics machine learning written 19 months ago by michealsmith • 740 • updated 19 months ago by Philipp Bayer ♦ 5.7k
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Comment: C: Abnormal pair orientation in RNA-seq data
... Yes, there are. But the read pair orientation doesn't make sense to me here that they suggests circular RNA. ...
written 19 months ago by michealsmith • 740
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Comment: C: Abnormal pair orientation in RNA-seq data
... The read pairs are mapped onto two exons, which are unique sequence. .So mapping is perfect. However, I just put an update to post; the middle intron is highly repetitive; which makes me feel possibly the intron is doing strange things to induce structural change? ...
written 19 months ago by michealsmith • 740
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Comment: C: Abnormal pair orientation in RNA-seq data
... Yes the remaining are normal (FR), but the coverage here is around 100X ...
written 19 months ago by michealsmith • 740
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Comment: C: Abnormal pair orientation in RNA-seq data
... Scale is around 1-2kb. I'm wondering if "strange things" indicate functional noncoding RNA, which is usually expressed in low level ...
written 19 months ago by michealsmith • 740
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Comment: C: Abnormal pair orientation in RNA-seq data
... Yes I also think about circular RNA; but circular RNA usually indicated by opposite-oriented read pairs facing outward(just like tandem duplication). I'm newcomer to circular RNA, maybe this also indicates circular RNA? ...
written 19 months ago by michealsmith • 740
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Comment: C: Abnormal pair orientation in RNA-seq data
... No, only small subsets are like this. Just normal standard Illumina paired-end sequencing; no strand-specificity ...
written 19 months ago by michealsmith • 740
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Abnormal pair orientation in RNA-seq data
... Hi biostarers, please see the attached picture from RNA-seq of total RNA; that read pairs with the same orientation (RR) that span two adjacent exons. (Supposedly we should see opposite orientation LR for paired-end reads) I know this indicates inversion for DNA sequencing; but what about in RNA-se ...
rna-seq inversion igv written 19 months ago by michealsmith • 740
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Allele-specific quantification methods for short tandem repeats?
... Hi, I would like to get very accurate quantification of the amount of different alleles of short tandem repeats. For example in DNA pool, at one locus, there could be 20% CA, 50% CACA， 30% CACACA, so what could I do？I don't think general SYBR green qPCR could work ...
allele microsatellite qpcr pcr written 24 months ago by michealsmith • 740

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