User: seta
seta • 920
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Posts by seta
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... Thank you for your response. As far as I know, TMM is between-sample normalized count (not break the assumption that you mentioned, please correct me if I'm wrong), and, therefore, more suitable for DE analysis, do you agree with me?
However, DEseq or edgeR has internally calculated TMM, but unfortu ...
written 22 days ago by
seta • 920
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... I asked about DEGseq, it differs from DEseq. ...
written 22 days ago by
seta • 920
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... Hi all,
Please kindly advise me if using **TMM method for read count normalization and then DEGseq** for identification of differentially expressed genes is the right approach?
I never this tool, but as I searched this package shouldn't be used for the analysis because its statistical assumptions a ...
written 22 days ago by
seta • 920
• updated
21 days ago by
theobroma22 • 930
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... Hi all,
I used pathway studio to construct a biological pathway of some selected DEG obtained from a RNA-Seq analysis. When I selected the shortest path, the tool gave me an error "Find short path algorithm requires exactly 2 entities in selection". But, I saw in papers used this algorithm with sev ...
written 6 weeks ago by
seta • 920
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... Never, not running with the same dataset. I checked all commands again. What should I do?!
Actually, the second dataset is those data that two read files of a single paired-end file had various length and I asked about it in this post ([enter link description here][1], and you kindly suggested to r ...
written 3 months ago by
seta • 920
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... Hi everybody,
I'm busy with genome-guided transcriptome assembly of some Illumina data from human. I used STAR for read mapping on hg19 and cufflinks for transcriptome assembly. I performed the analysis for two independent datasets, separately (one single end, 36bp and another, paired-end 100 bp). ...
written 3 months ago by
seta • 920
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... Thank you very much, h.mon ...
written 3 months ago by
seta • 920
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... Of course, google is the first one. To be honest, I saw the link, but unfortunately didn't get the point of interest. I'm looking for an image for understanding outer and inner genomic mapping coordinate, my problem is the concept of outer and inner, here, not detecting duplicates by mapping. ...
written 3 months ago by
seta • 920
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... Hi everybody,
Could you please kindly tell me what is the meaning and concept of outer in the below sentence? so sorry if you found the question is a basic, but I have to ask.
Toolkits for aligned reads use the **outer genomic mapping coordinates** of paired-end reads as an indication of identical ...
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... Hi all,
I read a sentence in a book about RNA-seq analysis, it says "Some aligners are able to distribute multimapping reads proportionally to the coverage between the equally matching locations".
Distributing of maultimapping reads based on the coverage between the equally aligned locations got ...
written 3 months ago by
seta • 920
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