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User: chris86

gravatar for chris86
chris86 • 250
Reputation:
250
Status:
Trusted
Location:
United Kingdom, London
Website:
https://intobioinforma...
Last seen:
1 week, 4 days ago
Joined:
3 years, 9 months ago
Email:
c*************@gmail.com

I am a post-doc data analyst working in London in stratified medicine.

Posts by chris86

<prev • 66 results • page 1 of 7 • next >
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Comment: A: TopHat mapping error
... Yeah you might use HISAT2 or STAR instead of Tophat. ...
written 19 days ago by chris86 • 250
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Comment: C: MSTRGs are plaguing my RNA-Seq analysis
... OK thanks, seems like a nice alternative to cuffmerge etc. ...
written 20 days ago by chris86 • 250
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Comment: C: MSTRGs are plaguing my RNA-Seq analysis
... Andrew, what is the best way to annotate my taco transcripts using my human reference .gtf? Like I need a gene ID and symbol for each one. I could use the co-ordinates and write a script, but what do you do? ...
written 20 days ago by chris86 • 250
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Comment: C: Stringtie merge generates close duplicates of original transcripts
... This is a good point, surely duplicating the transcriptome is going to screw up quantification of transcripts and differential expression downstream? Did you find an answer to this? ...
written 27 days ago by chris86 • 250
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Comment: C: Tools To Do the Alternative Splicing Analysis
... I see. That is also interesting about ballgown. I like your package btw, but the vignette and manual are full of many spelling errors you should correct. ...
written 29 days ago by chris86 • 250
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Comment: C: Tools To Do the Alternative Splicing Analysis
... Kristoffer, can I ask why you don't mention Sleuth and Ballgown which, as far as I understand, were developed for a transcript based differential expression analysis starting with transcript quantifications? Thanks. ...
written 4 weeks ago by chris86 • 250
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Answer: A: ConsensusClusterPlus for small sample
... I wouldn't bother consensus clustering with really small sample sizes like that because your statistical power is poor, IMO better to use standard hierarchical clustering with aheatmap or complexheatmap. I usually consensus cluster with large samples sizes like at least over 60. I think the resampl ...
written 4 weeks ago by chris86 • 250
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Comment: C: Highly uneven RINs, mapping rates, and methods to deal with this (normalisation,
... Thanks Ian, I didn't think there were a lot of good options, but I thought asking is a good idea in these situations. I think I'm probably going to exclude quite a lot of samples based on low mapping rates, high duplication rates, and using PCAs. ...
written 10 weeks ago by chris86 • 250
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Comment: C: Highly uneven RINs, mapping rates, and methods to deal with this
... I'm not sure whether it is validate mappings or gc bias correction that is lowering the mapping rates, but it seems those flags are generally recommended and I have used both. I also tried reducing read length to 75bp or mapping just single ended reads, but this did not increase the mapping rates. F ...
written 11 weeks ago by chris86 • 250
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Highly uneven RINs, mapping rates, and methods to deal with this (normalisation, salmon)
... Hi I have Illumina mRNA-seq samples where it seems because of low RINs (2-4) in a bunch of them compared to the others, I am getting very widely varying mapping rates (15%-70%) and therefore counts per sample (e.g. 8,000,000 mapped reads vs 40,000,000). Plus I can't really use RIN/mapping rate as a ...
salmon rna-seq normalisation written 11 weeks ago by chris86 • 250

Latest awards to chris86

Supporter 4 months ago, voted at least 25 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Deriving p values for gene correlations by permutation analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Deriving p values for gene correlations by permutation analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Limma contrast matrix help
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Limma contrast matrix help
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.9 years ago, created an answer that has been accepted. For A: Quick way to Identify batch effect from covariates?
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