User: amyfm

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amyfm10
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Ireland
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Posts by amyfm

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Comment: C: How to choose a TPM cut-off point
... But if I just want to know the total of transcripts detected, wouldn't it be enough to select the transcripts with TPM >1? ...
written 4.0 years ago by amyfm10
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Comment: C: How to choose a TPM cut-off point
... Thank you very much! So it is more difficult than I thought. I used DESeq2 for differential expression analysis, not edge R. So please, if I have my TPM file (all my transcrit IDs and the tpms and reads for each transcript) could you tell me how I create the logTPM histogram and calculate the numbe ...
written 4.0 years ago by amyfm10
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How to choose a TPM cut-off point
... Hi, After RNA seq, alignment, counting, and normalization of the counts (TPMs), finally I have a document representing a tissue at a particular condition with all the transcript IDs and TPMs. I have 2 questions: -If I just want to know how many transcripts are expressed in that tissue at the parti ...
tpm rna-seq transcript written 4.0 years ago by amyfm10
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How to use WEGO (Web Gene Ontology Annotation Plot)
... Hi, I have an excell file with around 1000 genes of interest to me and I want to do pathway analysis. I read about WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl), an online tool to get nice graphics of the pathways, but I don't know how to use it. I don't know which file I should upload. ...
pathway gene ontology wego written 4.0 years ago by amyfm10 • updated 21 months ago by lakhujanivijay4.5k
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goseq code after DESeq2 -NO IDEA!
... Hi, After DESeq2 analysis of my RNAseq data  in order to obtain differentially expressed genes between 2 cell types, I have a csv file with approximatelly 26000 genes, of which around 6000 genes are differentially expressed (padjustedvalue < 0.05). Now I want to use goseq in order to study pathw ...
deseq2 goseq script written 4.0 years ago by amyfm10
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Convert excel file with ensemble transcript IDs to Gene IDs
... Hi,   After differential expression analysis, I have a list of around 30.000 ensembl ID transcripts in an Excel file, and I would like to have the same list in the same order but with Gene IDs. I have been trying with David Ontology but I can't get to obtain it.   Do you know any practical way? ...
gene id excel transcript convert written 4.0 years ago by amyfm10 • updated 4.0 years ago by cycro270
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Comment: C: DESeq2 for differential expression analysis of RNA-seq datawith few samples per
... Thank you very much! With more than 2 replicates, you mean 2 replicates included? ...
written 4.0 years ago by amyfm10
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Comment: A: DESeq2 for differential expression analysis of RNA-seq datawith few samples per
... Thank you very much for your help.   Doing my differential expression analysis between 2 and 3 different animal models, I obtain fewer DEGs than if I do it between 3 and 3 (in this last case I am adding one sample that has regular quality - the others have good quality). My aim is obtaining as man ...
written 4.0 years ago by amyfm10
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Comment: C: DESeq2 for differential expression analysis of RNA-seq datawith few samples per
... thank you, according to that paper DESeq (and I imagine DESeq 2) have better performance than other methods when using few replicates ...
written 4.0 years ago by amyfm10
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Comment: A: DESeq2 for differential expression analysis of RNA-seq datawith few samples per
... My samples are ovarian tissue in different 2 conditions (high and low fertility), and as I said 2-3 replicates per condition When I try the differential expression analysis between only 2 samples (1vs1), I obtain a smaller list of genes than when I do it between 5 samples (2 vs 3), which makes me t ...
written 4.0 years ago by amyfm10

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