User: niuyw

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niuyw0
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Posts by niuyw

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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... Hi, It's an old thread but I found a paper talking about the quantification of RNA-seq data: [Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data][1]. In its conclution part, it said "Importantly, our analysis indicates that the explic ...
written 4 days ago by niuyw0
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Comment: C: tophat-cufflinks command pipeline
... Hi, It's an old thread but I found a paper talking about this recently: [Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data][1]. In its conclution part, it said "Importantly, our analysis indicates that the explicit quantification of t ...
written 4 days ago by niuyw0
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Comment: C: Finding the parent gene of pseudogene in mouse
... Thanks, Juke. It is very helpful. ...
written 4 days ago by niuyw0
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Comment: C: Finding the parent gene of pseudogene in mouse
... Hi Juke, if I want to find the parent gene of lots of pseudogenes using phylogeny method, is it acceptable using some simple method to infer the relations of sequences, such as a NJ tree? The ML tree needs a lot of computing resources. Comparing with a rigorous blast search (perform a blast search t ...
written 8 days ago by niuyw0
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Comment: C: Extract all bacteria sequences from the nr database
... Hi, shenwei. We could get the protein accession numbers from the [prot.accession2taxid.gz][1], but how to get the accession number of DNA sequence? There are several files under the url: [ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/][2], which one shoud be used? Thanks! [1]: ftp://ftp.nc ...
written 7 weeks ago by niuyw0
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Comment: C: Atlas -link inputs
... I am also having the same problem. Did you get an answer? ...
written 4 months ago by niuyw0
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Comment: C: Automated Plotting Of Seq. Reads In A Bam File
... What's in the igv.sh? bedToIgv can only generate a batch file for the IGV interface. I don't know how to run this in command line. Thanks! ...
written 5 months ago by niuyw0

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