User: soren.narges

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Posts by soren.narges

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Comment: C: experimental design in RNA-seq differential expression analysis
... Sorry if haven't been clear. By reference distribution I meant total number of detected genes in the experiment (# DE + # non-DE genes). ...
written 8 days ago by soren.narges0
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Comment: C: experimental design in RNA-seq differential expression analysis
... Yes, I meant when correcting for multiple testing in DE analysis, all the tags are used and that affects the fdr values and final list (number) of DE genes. But when performing e.g. Fisher exact test in enrichment analysis, only 80% of the tags (around 20% are unmapped and removed) are used as refer ...
written 9 days ago by soren.narges0
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Comment: C: experimental design in RNA-seq differential expression analysis
... Exactly, I was thinking of FDR values in both DE and enrichment analysis. Like, 20% of the background reference would be unmapped for enrichment analysis. But on the other hand the sample size is very small (3 per group) so I wanted to have more rows for data sharing while running DE analysis. But a ...
written 9 days ago by soren.narges0
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experimental design in RNA-seq differential expression analysis
... Hi, I am planning to run differential expression analysis and then enrichment analysis for an RNA-seq experiment from arabidopsis. The RNA-seq count table has TAIR tags/ids as rows. I was thinking that some of these tags are non-coding genes (e.g. micro RNA, etc) and so when converting TAIR ids to ...
experimnetal design de analysis rna-seq written 9 days ago by soren.narges0 • updated 9 days ago by i.sudbery10k
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Transcription start site (TSS) prediction in bacteria
... Hi, I am working on regulatory features in bacterial genome and was wondering to ask if anyone has experience with tools available for the transcription start site (TSS) prediction procedure. Currently, I am using TSSpredator but was wondering about other state-of-the-art options you could suggest ...
bacteria tss written 5 months ago by soren.narges0

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