User: Dario Strbenac
Dario Strbenac • 1.3k
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- 7 years, 3 months ago
- Email:
- d*************@sydney.edu.au
PhD student.
Posts by Dario Strbenac
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... You imported alignments whereas STAR's summary is in regard to reads. If a read can have more than one alignment, then 9 million reads can result in 20 million alignments because there is a 1:many relationship between them.
...
written 22 days ago by
Dario Strbenac • 1.3k
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... It's easy. For example,
library(GenomicAlignments)
ambiguousReads <- readGAlignmentPairs("/users/robert/project/example.bam", param = ScanBamParam(flag = scanBamFlag(isSecondaryAlignment = TRUE))) # Only import multi-mapping reads.
library(rtracklayer)
genesExonsTranscripts <- import("/user ...
written 23 days ago by
Dario Strbenac • 1.3k
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... Is it possible with Gviz to render Sashimi plots for two alignment tracks with one of the plots vertically flipped? This would mean that the zero value was in between the two tracks and the arcs of each track would be pointing out to opposite directions, so the arcs would be joined at the mid-line b ...
written 4 weeks ago by
Dario Strbenac • 1.3k
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... This is explained in the software's vignette. It seems that hardly any samples have details recorded about drug treatment, so it doesn't seem possible to incorporate patient treatment into your analysis. Perhaps another relevant dataset might be available from Gene Expression Omnibus and could have ...
written 5 weeks ago by
Dario Strbenac • 1.3k
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... What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to each batch individually, then, due to filtering of each count matrix on CPM, the resulting normalised value tables of each batch contain a different number of rows ...
written 3 months ago by
Dario Strbenac • 1.3k
• updated 3 months ago by
Aaron Lun • 15k
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Comment:
C: plotMDS Input Feature Filtering
... Certainly, I could. I wanted to see if there was an obvious batch effect before I applied batch effect correction, because I like to try and avoid between-sample normalisation if it's there's no clear difference. The first batch has 14 male and 4 female samples, whereas the second has 21 male and 21 ...
written 4 months ago by
Dario Strbenac • 1.3k
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... Indeed, after reading it again, I noticed that I interpreted it incorrectly.
...
written 4 months ago by
Dario Strbenac • 1.3k
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... I think that the current wording is confusing. The explanation states "This ensures that a gene will be retained if it is expressed in both the libraries belonging to any of the six groups.". I read this as the two samples will belong to the same class, whereas the filtering is independent of sample ...
written 4 months ago by
Dario Strbenac • 1.3k
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... When examining the most variable genes for a clinical cancer dataset generated as batches on different days, I notice that the genes are mainly ones located on the X and Y chromosomes such as XIST, UTY, and ZFY. Is it common practice to subset the matrix to remove these before making MDS plots, as t ...
written 4 months ago by
Dario Strbenac • 1.3k
• updated 4 months ago by
Gordon Smyth ♦ 30k
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... Another solution is to read the file twice, once with makeTxDbFromGFF and a second time with import.gff3. Then, the matching of IDs is easy and doesn't miss those newly discovered genes which GENCODE has annotated with symbols.
...
written 4 months ago by
Dario Strbenac • 1.3k
Latest awards to Dario Strbenac
Popular Question
29 days ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
4 months ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
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15 months ago,
voted at least 25 times.
Scholar
21 months ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion
4.3 years ago,
created 100 posts.
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