User: mforde84

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mforde84440
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Posts by mforde84

<prev • 93 results • page 1 of 10 • next >
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Comment: C: NGS Sequencing depths
... sorry, my bad, a misinterpretation on my end. ...
written 3 days ago by mforde84440
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Comment: C: Any better ways to filter GATK Mutect2 output?
... agreed. when people say stuff like the exonic mutation rate is on average 1 per kb, they are talking about germline calls. so if your looking at wgs or exome, then yea you might see 10s of thousands of events (the majority of which are probably non-synonymous and or high MAF). frequencies of somatic ...
written 3 days ago by mforde84440
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Comment: C: NGS Sequencing depths
... ah, i missed that. my bad. ...
written 3 days ago by mforde84440
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Comment: C: RNA-seq: bias in coverage
... I'm not sure you can really avoid the bias. If exon 1 on average has significantly higher CG content than exon N, then thats just the fact of the matter. ...
written 3 days ago by mforde84440
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Comment: C: analysing retrieved RNAseq datasets from GEO
... Related to what though? http://www.bioconductor.org/help/workflows/rnaseqGene/ ...
written 3 days ago by mforde84440
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Comment: C: NGS Sequencing depths
... You could even look into doing scale and quantile normalizations. This is commonly used in meta-analysis of chip data from different platforms or signal channels. Though it kinda feels like cheating in some sense for RNAseq. ...
written 3 days ago by mforde84440
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Comment: C: NGS Sequencing depths
... Remove them from analysis. That or you can downsample the more deeply sequenced librarys to a level consistent with the problematic batch. If you still see clear seperation on PCA after doing this, then it's likely a batch effect issue, and the samples should be discarded. ...
written 3 days ago by mforde84440
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Comment: C: NGS Sequencing depths
... pca is an unsupervised method. so in this instance it's just the two primary components which explain the largest amount of variability in the samples? ...
written 3 days ago by mforde84440
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Comment: C: Differences between Counts and FPKMS
... yep, completely agree. massively parallel sequencing is unfortunately very noisy especially for smaller and low abundance features. also i think this problem scales linearly with sequencing depth. in my opinion it's still a very "experimental" technology. ...
written 3 days ago by mforde84440
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Comment: C: Differences between Counts and FPKMS
... I've never seen differential expression ... ever ... :D. Just kidding. It depends. If your gene annotation has say 15000 genes, and 14000 are differentially expressed then yea, there's probably a problem. What you want are sanity checks. Do you see something that you should expect to see ... a posi ...
written 3 days ago by mforde84440

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