User: chris86
chris86 • 380
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... Try doing some example read alignments and then just trying to input the directory into R. I am having no problems with it, I'm using the latest version of salmon and not changing the output folder files and structure at all afterwards. ...
written 20 days ago by
chris86 • 380
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... If you are sure your output directories are as normal (they match example ones), then ask here for more help, https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues. ...
written 20 days ago by
chris86 • 380
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... OK, I think there is something different with your salmon output directories. I don't know what that is. Make sure your output directories contain all the files and folders normally outputted by salmon into a directory per sample. ...
written 20 days ago by
chris86 • 380
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... Can you work through the example data successfully first?
https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html
I suggest reading the section in the longer workflow called '
Importing Data from Kallisto, Salmon, RSEM or StringTie'. It is ...
written 20 days ago by
chris86 • 380
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... Yeah you don't need the BAM file anymore, you can just use the salmon counts with isoswitchanalyser.
If you want new gene models you can generate them using hisat2 and stringtie or strawberry, this is a lot more work and a different pipeline. People do this if they think their annotation is not tha ...
written 22 days ago by
chris86 • 380
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... If you mean isoform level transcript DE analysis you can use Sleuth (https://github.com/pachterlab/sleuth), accessible through the wasabi package (https://github.com/COMBINE-lab/wasabi). If you mean splicing analysis, it is better to use isoswitchanalyser in my opinion (https://bioconductor.org/pack ...
written 22 days ago by
chris86 • 380
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... May be better to pre-filter your data-set features based on the co efficient of variation. Your unlikely to need 50,000 features.
I also find the delta K with that method subjective to what constitutes the best number of clusters and it can't handle higher numbers of clusters. An alternative to thi ...
written 27 days ago by
chris86 • 380
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Comment:
C: DEXSeq With Reduced Annotations
... Can't see why that would matter unless you have pre-selected those genes due to a prior statistical test and therefore would be biasing your results. ...
written 5 weeks ago by
chris86 • 380
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... 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 ...
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... Your question is not specific enough.
Machine learning can mean a great number of things.
...
written 4 months ago by
chris86 • 380
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