User: niuyw

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niuyw20
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New User
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China/Beijing
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2 hours ago
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1 year, 8 months ago
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Posts by niuyw

<prev • 12 results • page 1 of 2 • next >
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Questions about de novo genome assembly from mixed DNA samples
... Hi, Recently I'm working on a *de novo* genome assembly project. Because the animal we study is so tiny, we had to pool DNA together from multiple individuals. And we've sequenced these DNA using both PacBio and Illumina. I've assemble the PacBio long reads into contigs, and want to do scaffolding ...
mixed dna samples hybrid reads genome assembly written 2 hours ago by niuyw20 • updated 20 minutes ago by lieven.sterck1.5k
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Comment: C: PCA tpm fpkm
... Hello vchris, Thank you for your discussions! Seeing many threads about the normalization/preprocessing, I want to put some code pieces here, and look forward to your comments and help. Comparing to DEG analysis, I care more about data preparation. library(Rsubread) library(edgeR) ...
written 3 months ago by niuyw20
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Comment: C: Preparing RNA-seq data for Hierarchical Clustering
... Thank you! I'm looking over your answers about PCA. They are very helpful, thanks again! ...
written 3 months ago by niuyw20
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Comment: C: Preparing RNA-seq data for Hierarchical Clustering
... Hi Kevin. I'm new to this. Sorry if this question is a bit basic. When referring to "normal distribution", it means "all genes' expression in one sample" or "one gene's expression in all samples"? ...
written 3 months ago by niuyw20
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Comment: C: Pathway Commons 2 - Search And Visualize Public Biological Pathway Information.
... Hi, Pathway Commons is a great database for gene associations. I have a simple question: can I extract interactions supported by experimental data? Thanks! ...
written 5 months ago by niuyw20
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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 5 months ago by niuyw20
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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 5 months ago by niuyw20
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Comment: C: Finding the parent gene of pseudogene in mouse
... Thanks, Juke. It is very helpful. ...
written 5 months ago by niuyw20
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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 5 months ago by niuyw20
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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 6 months ago by niuyw20

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