User: niuyw
niuyw • 20
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- China/Beijing
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- 4 weeks, 1 day ago
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- 2 years ago
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Posts by niuyw
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... Yes, I agree with you. Because I need to set a threshold to filter out contaminated contigs, I prefer to filter on the raw data now. Thank you very much~ ...
written 3 months ago by
niuyw • 20
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... The latest version of Kraken with default parameters was used, and the assembly was generated by Canu. According to the results of Kraken, about 75% contigs were classified into archaea, bacteria, or viral. I was also a bit shocked by this. The contaminated regions accounted for about 0.65% of the t ...
written 3 months ago by
niuyw • 20
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... I found more than 70% contigs were classified into contaminated sequences, but most of them only had a small part (several k-mers) contaminated. There would be a few sequences left if removing the whole contigs, so I want to mask the contaminated regions with 'N'. Maybe I shoud try remove contaminat ...
written 3 months ago by
niuyw • 20
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... Thank you for your answer! It's very clear. Now I can proceed. Thank you :)
I've got another question. Maybe I should open a new thread, but you may know the circumstances better. You know, because of the tiny sizes, we used the whole bodies for sequencing, so there are considerable sequence contam ...
written 4 months ago by
niuyw • 20
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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 4 months ago by
niuyw • 20
• updated
4 months ago by
lieven.sterck • 2.6k
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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 7 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 7 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 7 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 9 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 9 months ago by
niuyw • 20
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