User: weixiaokuan

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weixiaokuan80
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United States
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1 year, 3 months ago
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3 years, 5 months ago
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Posts by weixiaokuan

<prev • 30 results • page 1 of 3 • next >
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bioawk output in original fastq format
... Hi, I was trying to use bioawk to extract some matched sequences from a fastq file. However, the output is somehow tabular format of fastx with $name, $seq, $qual and $comment. Did anyone know if there is an option from bioawk which can make the output keep the original fastq 4 line format? I know ...
fastq bioawk written 16 months ago by weixiaokuan80 • updated 5 weeks ago by Stephane Plaisance380
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Comment: C: RNA-Seq without replicate using Kallisto
... Maybe I didn't make it very clear. I know it's no way to attain statistical evaluation. But I am wondering if there is any way to scale the data such as by lib sizes. I am thinking TPM from kallisto is one way to do it. -Xiaokuan ...
written 2.2 years ago by weixiaokuan80
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Comment: C: RNA-Seq without replicate using Kallisto
... by they way, will TPM from Kallisto help in this situation? ...
written 2.2 years ago by weixiaokuan80
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Comment: C: RNA-Seq without replicate using Kallisto
... totally understood. However, a lot of times, things are not controlled by us and sometimes the samples are just not enough. So I think a method for no replicates is very helpful. Thank you for all the help. -Xiaokuan ...
written 2.2 years ago by weixiaokuan80
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Comment: C: RNA-Seq without replicate using Kallisto
... to identify some trend of differentially expressed genes then we may perform further experiments to validate. ...
written 2.2 years ago by weixiaokuan80
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Comment: C: RNA-Seq without replicate using Kallisto
... I know. But I want to have some measurement anyway, especially after some normalization/scaling. Not all the experiments have full replicates. ...
written 2.2 years ago by weixiaokuan80
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RNA-Seq without replicate using Kallisto
... Hi, I have a project using RNA-Seq but there are no replicates for each condition. I am wondering what method I should use for such a situation. Especially, how I should normalize the data? Apparently, I cannot use limma-voom pipeline. It seems I may be able to use DESeq2. But I am wondering if it's ...
kallisto rna-seq written 2.2 years ago by weixiaokuan80
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Comment: C: WGCNA maxBlockSize limit
... Answer by Peter Longfelder from bioconductor fourm: "The limit is (the square root of) the maximum matrix size addressable by a 4-byte pointer. I will eventually update the WGCNA code to remove the limit, but for now it is what it is. The limit is independent of how much memory you have. Sorry! Pet ...
written 2.4 years ago by weixiaokuan80
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Comment: C: WGCNA maxBlockSize limit
... yes, I used microarray. ...
written 2.4 years ago by weixiaokuan80
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Comment: C: WGCNA maxBlockSize limit
... it has about 600G memory on the node I was using. ...
written 2.4 years ago by weixiaokuan80

Latest awards to weixiaokuan

Great Question 22 months ago, created a question with more than 5,000 views. For which normalized counts is better from DESeq2
Popular Question 22 months ago, created a question with more than 1,000 views. For illumina EPIC array support by R packages?
Popular Question 23 months ago, created a question with more than 1,000 views. For illumina EPIC array support by R packages?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For which normalized counts is better from DESeq2

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