User: kristoffer.vittingseerup
kristoffer.vittingseerup • 3.5k
- 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
... 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.vittingseerup • 3.5k
0
votes
1
answer
869
views
1
answers
... 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.vittingseerup • 3.5k
0
votes
1
answer
268
views
1
answers
... 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.vittingseerup • 3.5k
0
votes
1
answer
472
views
1
answers
... 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.vittingseerup • 3.5k
1
vote
2
answers
642
views
2
answers
... 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.vittingseerup • 3.5k
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.vittingseerup • 3.5k
0
votes
1
answer
508
views
1
answers
... 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.vittingseerup • 3.5k
0
votes
1
answer
1.5k
views
1
answers
... 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.vittingseerup • 3.5k
0
votes
2
answers
9.1k
views
2
answers
... 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.vittingseerup • 3.5k
0
votes
1
answer
341
views
1
answers
... 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.vittingseerup • 3.5k
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?
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: How to deal with the case that one gene symbol matches multiple ensembl ids?
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?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: How to deal with the case that one gene symbol matches multiple ensembl ids?
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
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Scholar
16 months ago,
created an answer that has been accepted.
For A: which option is better for DESeq2 analysis: salmon or htseq-count?
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