User: omicsnstuff

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Posts by omicsnstuff

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RNASeq relative isoform usage across batches
... I'm looking for input from experts on RNA-seq about the comparison of isoform ratio across different batches. Assuming all things are equal when considering RNA isoform allocation of reads from RNASeq, could it be argued that the relative abundance of isoforms of a gene could be compared between d ...
rna-seq written 4 days ago by omicsnstuff0
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Comment: C: Removing strandedness information for analysis RSEM/STAR/
... I've edited the post, is this clearer? ...
written 4 weeks ago by omicsnstuff0
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Comment: C: Removing strandedness information for analysis RSEM/STAR/
... I've edited the post, hopefully my problem is clearer? ...
written 4 weeks ago by omicsnstuff0
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Comment: C: Removing strandedness information for analysis RSEM/STAR/
... I was informed that normalising using TPM's allowed for this type of inter batch comparison? Is that incorrect? ...
written 4 weeks ago by omicsnstuff0
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Removing strandedness information for analysis RSEM/STAR/
... Hi all, I've sequenced a good number of patient samples as per the best protocol for assessment of splicing and DGE and moving forward as I was advised to do, with using the GTEx data as control. I'm now noticing the gene expression is not analogous between these batches, many genes are not expres ...
transcriptomics rna star rsem rna-seq written 4 weeks ago by omicsnstuff0
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OUTRIDER RNASeq Gencode annotation
... I'm assessing the utility of outrider for RNASeq diagnostics. My count table is generated using the gencode annotation I'm not sure how to set this up as an object which I can use in the OUTRIDER syntax for pre-processing steps. I'm a relative novice with R and am running through Linux OS. I hav ...
outrider R rna-seq written 12 weeks ago by omicsnstuff0 • updated 12 weeks ago by felix.brechtmann0
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Comment: A: HTSeq output Gene format unfamiliar
... bump bump bump does anyone have any ideas about this, or has anyone seen it before. ...
written 4 months ago by omicsnstuff0
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HTSeq output Gene format unfamiliar
... I'm experiencing an unusual output format from htseq I haven't seen previously Instead of just the stable gene-id, I get the stable gene ID plus an underscore and a single numerical digit. as below: ENSG00000003096.14_4 Does anyone know why this is happening, how I can remove them from the proc ...
htseq gene name rna-seq written 5 months ago by omicsnstuff0
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Answer: A: OUTRIDER for gene expression outliers (could not find function "OutriderDataSet"
... I'm not able to remember unfortunately. Instead I installed ran the program through linux and it worked fine. I shall try reinstalling. ...
written 5 months ago by omicsnstuff0
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OUTRIDER for gene expression outliers (could not find function "OutriderDataSet")
... Hi all, This is my first post on here, and I haven't been able to find any other examples of problems with Outrider so far. I'm still hopeful someone might have the smarts to help me solve this issue. I'm trying to run my very first OUTRIDER script in RStudio, but I keep getting an error message ...
R bioconductor rna-seq sequencing written 5 months ago by omicsnstuff0

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