User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 482 results • page 1 of 49 • next >
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Answer: A: Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
... StringTie annotation can have 2 problems: 1) Unassigned gene_name in single gene: It is a novel transcript in a known gene 2) Cluster of genes (multiple gene_names/gene_ids) which are joined together by StringTie because of their overlap in genomic space. Lastly you can find novel genes which will a ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: Resolving expression profiles of genes with same name but different MSTRG ID
... The problem with gene_names in StringTie data can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks because of their overlap 3) It is a novel gene - ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: I get different ENSG IDs for the same MSTRG ID
... You seem to have cases of merged genes. Basically some genes are joined together by StringTie/Cufflinks because of genomimc overlap of associated transcripts. To solve this I have just release an update to the R package [IsoformSwitchAnalyzeR][1] (available in >1.11.6) which can fix problem 1 an ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: Stringie output doesn't have any gene names!
... I just wanted to post an addition to my comment above: The missing gene_names from StringTie can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks b ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: gene IDs in stringtie output
... The missing gene_names from StringTie can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks because of their overlap 3) It is a novel gene - meaning ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: StringTie --merge creates the same id for neighbouring genes
... The missing gene_names from StringTie can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks because of their overlap 3) It is a novel gene - meaning ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: StringTie - A transcript matching to multiple genes
... The missing gene_names from StringTie can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks because of their overlap 3) It is a novel gene - meaning ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Answer: A: How to deal with MSTRG tag without relevant gene name?
... The missing gene_names from StringTie can originate from 3 different sources: 1) It is a novel transcript in a known gene 2) It is a novel transcript in a cluster of genes (multiple gene_names) which are joined together by StringTie/Cufflinks because of their overlap 3) It is a novel gene - meaning ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Comment: C: Ambiguous results of RNA-Seq data using stringtie with edgeR
... Did you run StringTie --merge as well? You can read more about the workflow [here][1]. And yes if you have a suspicion you migh have novel transcripts I recommend running StringTie. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR. ...
written 9 weeks ago by kristoffer.vittingseerup3.4k
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Comment: C: Packages in R for analyze premature stop codon and GC contents
... IsoformSwitchAnalyzeR can work directly from the "rsem.isoforms.results". I suggest you take a look at the [quick start][1] part of the vignette which should describe exactly what you need including code you can use. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyz ...
written 3 months ago by kristoffer.vittingseerup3.4k

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