User: Tao

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Tao210
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Posts by Tao

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Calculating TPM Values
... In your example, featureCount would give the length of union of these three exons. You can read the `7.2.8 Program output` part in [featureCount manual][1], which I also paste here: > Column ‘Length’ always contains one single value which is the total > number of non-overlapping bases include ...
written 6 weeks ago by Tao210
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Answer: A: Calculating TPM Values
... Hi biocool2018, You don't need to rerun everything. The read count table is enough to calculate TPM table. The thing is, you might need to use the length of union of exons instead of using the gene length. Please see [here][1] for the source code transforming reads count to TPM. The following cod ...
written 6 weeks ago by Tao210
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Answer: A: RNA-seq: Explain STAR quantMode geneCounts values
... Thanks for the explanations! Here is my understanding: column 3 and column 4 are corresponding to different strand-specific library preparation protocol. Please see HTSeq `-s/--stranded` description as follows. [This blog][1] explains the read orientations in different strand-specific/un-stranded ...
written 6 weeks ago by Tao210
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Comment: C: WGCNA signed vs unsigned network
... For co-expression network, I would prefer unsigned weight. But you can try both, to find out which result looks more meaningful. ...
written 5 months ago by Tao210
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Answer: A: WGCNA signed vs unsigned network
... I think the "sign" represents the sign of weight on the edges. If you care about the sign, for example sign represents positive or negative regulation between two nodes, then you need to choose "signed". On the other hand, if the weight just represent the strength of relatedness between two nodes, y ...
written 5 months ago by Tao210
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Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
... That is for detecting non-biallelic variants. For example, one SNP might has 3 alleles: A -> C, A -> G. And the this step will report such SNPs as mis-match SNPs. ...
written 5 months ago by Tao210
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Answer: A: What exactly is sequencing depth in RNAseq?
... I want to give you a very intuitive but maybe not very accurate explanation: You can imagine each base (A/G/C/T) is a grain of rice. Suppose you sequenced a big of rice (say 100M bases), and then fill them into a very narrow but very long rice box with width = 1 grain of rice. The rice height in th ...
written 6 months ago by Tao210
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Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
... Thanks so much for your suggestions and reference! That's very helpful! This dataset is one of several datasets I used in my project, which need genotypes on whole genome, not only gene nearby regions. Luckily, we just find the genotype data call from WGS is now available for that dataset. So, that' ...
written 6 months ago by Tao210
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Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
... Hi Kevin, Thanks! You are right. Imputation can be done without any error, but how accurate it would be?That's exactly what I concerned! Thanks for your references. Best, Tao ...
written 6 months ago by Tao210
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Comment: C: Imputation on two genotyping datasets: should I do imputation separately? or mer
... For this question, in case someone would have similar situation, I'd like to answer by myself. In GTEx (v6p) protocol, they use two different genotyping array: OMNI 5M for pilot phase and OMNI 2.5M for Mid-phase. They first downsized the 5M to 2.5 M portion of variants, and then did QC and imputatio ...
written 6 months ago by Tao210

Latest awards to Tao

Popular Question 27 days ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 4 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 5 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Scholar 5 months ago, created an answer that has been accepted. For A: How to choose NCBI viral database?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 8 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 12 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 22 months ago, voted at least 25 times.
Scholar 2.0 years ago, created an answer that has been accepted. For A: How to choose NCBI viral database?

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