User: niuyw
niuyw • 20
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- China/Beijing
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Posts by niuyw
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... 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 ...
written 2 hours ago by
niuyw • 20
• updated
20 minutes ago by
lieven.sterck • 1.5k
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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
niuyw • 20
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... Thank you! I'm looking over your answers about PCA. They are very helpful, thanks again! ...
written 3 months ago by
niuyw • 20
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... 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
niuyw • 20
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... 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
niuyw • 20
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... 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
niuyw • 20
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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
niuyw • 20
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... Thanks, Juke. It is very helpful. ...
written 5 months ago by
niuyw • 20
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... 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
niuyw • 20
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... 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
niuyw • 20
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