User: Chris Cabanski

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Posts by Chris Cabanski

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Tophat Rna-Seq Mapping Quality
... I agree that you can get uniquely reads quicker using samtools, assuming that you are confident in the mapping qualities. I was looking at metrics beyond counting/extracting the uniquely aligned reads, and I was using output from several different aligners, so I wrote a perl script for this task. ...
written 6.6 years ago by Chris Cabanski330
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Comment: C: Tophat Rna-Seq Mapping Quality
... I've never fully trusted the mapping quality scores, so when I am interested in uniquely mapped reads I filter based on the SAM tags. I know that for TopHat v1.4.1 onwards (I haven't looked at earlier versions), the number of mappings for each read is reported in the "NH" tag, so you can write a si ...
written 6.6 years ago by Chris Cabanski330
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Comment: C: The Easiest Way To Produce The Normalised Counts In Edger
... I've used predFC() in the past, which produces normalized counts similar to microarray values. Not sure how different this output is from cpm(). ...
written 6.7 years ago by Chris Cabanski330
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Comment: C: Why Does Cufflinks With Mask (-M) Option Have Lower Fpkm For Mrna Genes?
... It looks like this might be related to the options --compatible-hits-norm and --total-hits-norm. The documentation isn't super clear, but I'd suggest playing around with these options and seeing what happens. ...
written 6.7 years ago by Chris Cabanski330
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Answer: A: Is It Possible To Fix The Scale In Ggplot?
... You will need to make 2 modifications. Let's suppose that you want your scales to go from -4 to 4: Change all data values less than -4 or greater than 4 so that they are equal to 4 (otherwise they will be colored grey) Add "limits" to your scale_fill command: ... + scale_fill_gradientn(colours=c ...
written 6.8 years ago by Chris Cabanski330
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Answer: A: How To Determine If A Gene Has A Low Intensity/Expression In Microarrays ?
... When analyzing Affymetrix human exon arrays, I've used the DABG (detected above background) function from the Affymetrix power tools software. This provides a p-value for each probe after testing whether or not a probeset is detected above background. When using gene-level estimates, a threshold c ...
written 6.8 years ago by Chris Cabanski330
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Comment: C: How Can I Get Deg From Rsem In Tcga'S Data?
... I would use the raw counts - edgeR and DESeq have their own normalization steps. ...
written 6.8 years ago by Chris Cabanski330
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Answer: A: How Can I Get Deg From Rsem In Tcga'S Data?
... I haven't actually looked at these files, but it sounds like '_expression_rsem_gene_normalized.txt' is probably what you want. The authors mention in their RSEM paper that their output includes 2 values: (1) an estimate of the number of fragments that are derived from a given isoform or gene (simil ...
written 6.8 years ago by Chris Cabanski330
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Comment: C: Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
... I haven't tried using RSEM values when finding DE genes, so I can't comment whether values should be log transformed. (FPKM values typically look more Gaussian when log transforming, so my gut reaction would be to log transform, but this should be tested). The authors mention that their output i ...
written 6.8 years ago by Chris Cabanski330
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Comment: C: Unable To Replicate Splice Junction In Tophat
... This region appears to be highly repetitive (looking at RepeatMasker track in UCSC). My guess is that the reads are mapping to more than 2 locations, so the "--max-multihits 2" command is causing the alignment to not appear. Have you tried to Blat one of the reads to see how many results come up? ...
written 6.8 years ago by Chris Cabanski330

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