User: kristoffer.vittingseerup
kristoffer.vittingseerup • 100
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Posts by kristoffer.vittingseerup
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... That is a correct assumption and tools do not check these names. That is also why if you use tools that filter for quality you get 4 files: 2 paired and 2 unpaired. That said I've acutally had problems with propper pairing in the past so it is a good thing always to check the first sequences (basica ...
written 2 days ago by
kristoffer.vittingseerup • 100
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... I can interpret your question in three different ways:
1. You are interested in changes in splicing because such a changes could give a cancer an advantage - aka transcript/isoform switches.
2. You are interested in novel transcripts identified only in cancers.
3. You are interested in whether a ...
written 2 days ago by
kristoffer.vittingseerup • 100
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... IsoformSwitchAnalyzeR (which I presume you are asking about) does not (yet) have the functionality. But another of my tools can do this: http://bioconductor.org/packages/spliceR/ - but you would need to combine the results manually.
Why are you interested in those coordinates? ...
written 2 days ago by
kristoffer.vittingseerup • 100
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... You can use ggplot2 by creating a facet for eact chromosome (with facet_wrap() ). ...
written 3 days ago by
kristoffer.vittingseerup • 100
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Answer:
A: Bamfile first step analysis
... I would recomend the R package Rsubread ( http://bioconductor.org/packages/Rsubread/ ) which allows you to quantify the genes in a BAM file thereby obtaining a count matrix for differential expression analysis. More specifically check the featureCounts() function. ...
written 6 days ago by
kristoffer.vittingseerup • 100
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... One possible explanation is that you have "to many" differentially expressed genes in the sense that if 30-50% of your detected genes are differentially expressed it is very hard to have large enrichments. I would try using a more strict DE cutoff by for example filtering on the log2FCs. ...
written 6 days ago by
kristoffer.vittingseerup • 100
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... Unfortunatly RefSeq does not have gene ids that group transcript ids together. The NM_xxxxx should be viewed as a transcript id so you will have to use the gene name or all transcript ids as a refrence.
On a sidenote unless you have a very specific reason I would suggest that you use another databa ...
written 9 days ago by
kristoffer.vittingseerup • 100
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... Alternatively you can just reduce all the gene to the transcription start site (or other point of interest) and then use GRanges with the approach you suggest ...
written 9 days ago by
kristoffer.vittingseerup • 100
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... That was a lot of questions. Let me give it a try:
1: This is due to two things: Of less interest is that the tools might use different pseudo counts. The major difference is that DESeq2 also uses bayesian information sharing in the estimation of the Log2FC to get more robust results. You can find ...
written 9 days ago by
kristoffer.vittingseerup • 100
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... Could you clarify what type of sequencing and what your aims are? (I'm guessing RNA-seq and gene expression analysis but it's not clear) ...
written 11 days ago by
kristoffer.vittingseerup • 100
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