User: kristoffer.vittingseerup

Reputation:
3,500
Status:
Trusted
Location:
European Union
Twitter:
@kvittingseerup
Last seen:
3 months ago
Joined:
5 years, 11 months ago
Email:
k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 483 results • page 1 of 49 • next >
3
votes
2
answers
268
views
2
answers
Answer: A: Quantify Isoforms in RNA-Seq data
... I have written a discussion of different tools [here][1]. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-quantification-tools-should-i-use ...
written 3 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
869
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
268
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
472
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
1
vote
2
answers
642
views
2
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
2.2k
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
508
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
1.5k
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
2
answers
9.1k
views
2
answers
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 5 months ago by kristoffer.vittingseerup3.5k
0
votes
1
answer
341
views
1
answers
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 5 months ago by kristoffer.vittingseerup3.5k

Latest awards to kristoffer.vittingseerup

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 7 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Scholar 8 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics vs. the Climate Crisis
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics vs. the Climate Crisis
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Fold change - a final explanation
Scholar 9 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Tools To Do the Alternative Splicing Analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 11 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 14 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 15 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics vs. the Climate Crisis
Pundit 15 months ago, created a comment with more than 10 votes. For C: Bioinformatics vs. the Climate Crisis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 15 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Tools To Do the Alternative Splicing Analysis
Scholar 16 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1419 users visited in the last hour
_