User: k.vitting.seerup

Reputation:
100
Status:
Trusted
Location:
European Union
Last seen:
5 days, 13 hours ago
Joined:
4 years, 4 months ago
Email:
k***************@gmail.com

Posts by k.vitting.seerup

<prev • 44 results • page 1 of 5 • next >
1
vote
1
answer
60
views
1
answers
Answer: A: Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rect
... Hi Asmita Thanks for reaching out. You describe an interesting, but very hard to implement, idea as switches in two different genes could use different groupings. IsoformSwitchAnalyzeR unfortunately does not support such analysis - it requires the groupings up front. Doing all possible devisions of ...
written 12 days ago by k.vitting.seerup100
0
votes
1
answer
60
views
1
answers
Comment: C: Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rect
... Could you elaborate on what you mean by "recurrently occurring switches"? ...
written 13 days ago by k.vitting.seerup100
0
votes
1
answer
409
views
1
answers
Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... For trimming I am using [Trimmomatic][1] and it does not specifically matter which filtering you are doing but when you trim paired data the result is 4 files (see "Paired End Mode" section of the [manual][2]) two which contains the ordered paired reads and two files containing respectively the left ...
written 5 months ago by k.vitting.seerup100
0
votes
1
answer
409
views
1
answers
Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... I think you might have mis-understood me due to me not being clear - sorry about that :-). What I am talking about is not mixing single-end and paire-end libraries. I am talking about the case where a paired end library where trimming of low quality reads etc (via e.g. Trimmomatic) causes the remova ...
written 5 months ago by k.vitting.seerup100
0
votes
1
answer
409
views
1
answers
Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... Hi Yang Thanks for clarifying this - and yes you are right it contain a mixture of paired and unpaired reads. Why would featureCounts not support mixed paired or unpaired reads? Means that if I have paired end data that needs trimming I will throw away a lot of data - often 5-15%... I think I was ...
written 6 months ago by k.vitting.seerup100
3
votes
1
answer
409
views
1
answer
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... **Summary** It seems featureCounts under certain circumstances ignores the ```isPairedEnd = TRUE``` argument. **Background** I have been using featureCounts successfully for many years but recently ran into a problem in files where I have a mixture of paired and unpaired strand specific data (P ...
rsubread featurecounts written 6 months ago by k.vitting.seerup100 • updated 5 months ago by Wei Shi3.2k
0
votes
1
answer
199
views
1
answers
Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... That is a known problem. UCSC does not have gene_ids which means you cannot directly use the with IsoformSwitchAnalyzeR (since it relies on gene_ids). So you would need to manually "concatenate" transcripts into genes. There are some lists hidden somewhere on UCSC where you can find txid conversion ...
written 6 months ago by k.vitting.seerup100
1
vote
1
answer
199
views
1
answers
Answer: A: error in aSwitchlist (isoformswitchanalyzeR)
... Thanks for clarifying versions above. The problem is that I have hardcoded the min Jaccard similarity of the annotation and the quantification to prevent people from using the wrong annotation with their quantifications. And as you can see the JC similarity is 0.948 (so close). When I recalculate it ...
written 6 months ago by k.vitting.seerup100
0
votes
1
answer
199
views
1
answers
Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Could you try updating to 1.5.6 (from the devel branch) and see if the problem persists? You can find the installation instructions [here][1]. Remember to restart your R session after the update. Cheers Kristoffer [1]: https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html ...
written 6 months ago by k.vitting.seerup100
0
votes
1
answer
199
views
1
answers
Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Which version of IsoformSwitchAnalyzeR are you using? Cheers Kristoffer ...
written 6 months ago by k.vitting.seerup100

Latest awards to k.vitting.seerup

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 337 users visited in the last hour