User: jomaco

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jomaco190
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Posts by jomaco

<prev • 54 results • page 2 of 6 • next >
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Cuffdiff secondary alignments (lower counts?)
... Hi, When I use the option --report-secondary-alignments in TopHat, cuffdiff reports that there are fewer fragments mapping to some genes in the genes.count_tracking file. Without any filtering following TopHat I would expect counts to be increased in most cases when using the -report-secondary-ali ...
unique secondary alignments tophat cuffdiff written 5.3 years ago by jomaco190 • updated 4.2 years ago by bodington0
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Comment: C: K-means for non-spherical (non-globular) clusters
... Yes, when the depth gets really high I don't really care how high it gets, so this seems ok given that I am expecting two "clusters" (see below), but as you point out they are not very cluster like, the data points are just separated, so it may be the case that I could apply something more simple. ...
written 5.3 years ago by jomaco190
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Comment: C: K-means for non-spherical (non-globular) clusters
... The common biological feature is that the genomic regions represented by the small (musty yellow?) group are expected to have no reads mapping (the organisms from which they were sampled are known to lack these regions). However, a certain amount of incorrect mappings would be expected so it is not ...
written 5.3 years ago by jomaco190
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Comment: C: K-means for non-spherical (non-globular) clusters
... I am happy with the result, I guess the question is whether it is reasonable to partition the data into the two clusters on the basis that they are more closely related to each other than to members of the other group (given that the clusters are non-spherical, but taking in mind that two groups wou ...
written 5.3 years ago by jomaco190
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Comment: C: K-means for non-spherical (non-globular) clusters
... Thanks Karl, I have updated my question with a graph of the clusters. It would be great if you could comment on whether  thelog transform is appropriate and whether the clusters seem reasonable given that two sets would be expected - one relating to regions which in reality should have zero coverage ...
written 5.3 years ago by jomaco190
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Zero expression Cuffdiff - conversative cut-off
... Hi, In the Cuffdiff gene_exp.diff file, I am looking for genes with zero FPKM for one of my samples and some level of expression in the other sample. If I was to take all of the genes with FPKM >0 for one sample and exactly zero FPKM for the other, then I would hopefully have all of the genes s ...
cut-off expression cuffdiff written 5.3 years ago by jomaco190
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K-means for non-spherical (non-globular) clusters
... I am not sure whether this would be more appropriate on a stats forum, but I feel some here may have knowledge of this. It is said that K-means clustering "does not work well with non-globular clusters." However, is this a hard-and-fast rule - or is it that it does not often work? I have a 2-d da ...
k-means spherical clusters written 5.3 years ago by jomaco190 • updated 5.3 years ago by mikhail.shugay3.4k
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Comment: C: GO term enrichment
... The clusters of interest only have a small subset of all the genes in the genome. However, the whole genome was used in the clustering process (therefore, the clusters of interest could potentially have contained all genes in the genome). So from how I interpret your answer, this means I am therefo ...
written 5.5 years ago by jomaco190
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GO term enrichment
... Hi, I am carrying out GO term enrichment on a set of up-regulated genes, and also on species-specific (OrthoMCL) gene clusters, and clade-specific gene clusters. I need to use a custom background of genes. For enrichment within the up-regulated genes can I simply take all the GO terms present in ...
go term enrichment gene ontology go written 5.5 years ago by jomaco190 • updated 5.5 years ago by Jean-Karim Heriche22k
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Comment: C: AUGUSTUS principal isoform
... Don't think I'm supposed to say - but it's a species in the asterids if that helps, newly sequenced ...
written 5.5 years ago by jomaco190

Latest awards to jomaco

Popular Question 4.3 years ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Deseq - Should I Include Only The Samples Being Compared?
Student 4.4 years ago, asked a question with at least 3 up-votes. For Deseq - Should I Include Only The Samples Being Compared?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 4.5 years ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Which Genome Synteny Program?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Which Genome Synteny Program?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For GO term enrichment
Supporter 5.3 years ago, voted at least 25 times.
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Deseq2 Pairwise Comparison Between Conditions
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Deseq2 Pairwise Comparison Between Conditions
Student 6.8 years ago, asked a question with at least 3 up-votes. For Deseq - Should I Include Only The Samples Being Compared?

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