User: kristoffer.vittingseerup
kristoffer.vittingseerup • 3.4k
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Posts by kristoffer.vittingseerup
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... 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.vittingseerup • 3.4k
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... 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.vittingseerup • 3.4k
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... 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.vittingseerup • 3.4k
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... 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.vittingseerup • 3.4k
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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.vittingseerup • 3.4k
0
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1
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386
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... 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.vittingseerup • 3.4k
0
votes
1
answer
1.4k
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1
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... 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.vittingseerup • 3.4k
0
votes
2
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8.2k
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... 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.vittingseerup • 3.4k
0
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1
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251
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... 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.vittingseerup • 3.4k
0
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1
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284
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... 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.vittingseerup • 3.4k
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