User: Jack

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Jack0
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Posts by Jack

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Explainnation of featureCounts in-built annotation?
... Hi all, I use featurecounts first to get the summary of the counts and the annotation, below are the codes: test<-featureCounts(files="test.bam", annot.inbuilt="mm10", annot.ext=NULL, isGTFAnnotationFile=FALSE, GTF.featureType="exon", GTF.attrType="gene_id", chrAliases=NULL, useMetaFeatures=TR ...
rnaseq annotation featurecounts written 13 months ago by Jack0 • updated 13 months ago by Wei Shi2.9k
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... The criteria I choose are either too strong or too weak. Maybe this is the problem. I thought it was not so important to choose the criterion so I just chose them randomly... ...
written 13 months ago by Jack0
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... Thank you for your great answer! You are right, both of the two criteria are too strong or two weak. I thought it was not so important to choose the criterion so I just chose them randomly... ...
written 13 months ago by Jack0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... Thank you Gordon Smyth! Your answer makes me clearer and better understand this problem! ...
written 13 months ago by Jack0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... I am just curious and want to understand the problem which I think is hard to understand. If the unstranslated regions are not useful for the gene's expression values (which I hope correspond to protein levels), I don't think there is a problem to throw them away. On the other hand, if not throwing ...
written 13 months ago by Jack0
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... In the workflow of edgeR I found it used "keep <- rowSums(cpm(y)>0.5) >= 2". It said "As a rule of thumb, we require that a gene have a count of at least 10–15 in at least some libraries before it is considered to be expressed in the study." Its library size is a little smaller than mine. S ...
written 13 months ago by Jack0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... What I am going to measure is the gene's expression values (which I hope correspond to protein levels). ...
written 13 months ago by Jack0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... In my understanding, CDS is more meaningful, since differential expression at the CDS level indicates potentially different protein outputs...Is this acceptable? Does this behavior have big flaws? ...
written 13 months ago by Jack0
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Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
... I have a set of RNA seq data with replicates of 2 for each condition. The library sizes range from 16970950 to 36720407 (shown below). > DGEList$samples     group lib.size norm.factors A1     A   31271688            1 A2     A   36720407            1 B1     B   16970950            1 B2     B   2 ...
rnaseq edger written 13 months ago by Jack0
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When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
... When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?   ...
rnaseq edger deseq2 featurecounts written 13 months ago by Jack0 • updated 13 months ago by Gordon Smyth35k

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