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User: Tao

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Tao • 300
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Posts by Tao

<prev • 67 results • page 1 of 7 • next >
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How to do Meta-analysis of statistics from T-tests and Wilcoxon rank sum tests?
... Hi Super stars, I have 6 datasets, and each dataset has two groups of values (~100 values in each group). I want to measure if the mean of values in the two groups are significantly different. First, I tested whether each dataset follows a normal distribution. If yes, t-test was performed, otherwis ...
meta analysis wilcoxon rank sum t test written 12 days ago by Tao • 300
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Answer: A: "hrc-1000g-check-bim.py" Unable to open specified bim file
... Hi, I remember it needs to specify the suffix of bim file. Such as: perl HRC-1000G-check-bim.pl -b data.bim -f data.frq -r HRC.r1-1.GRCh37.wgs.mac5.sites.tab -h ...
written 12 days ago by Tao • 300
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How to define the LD interval where a SNP locates?
... Hi all stars, Given a SNP, I want to define the LD interval that the SNP locates. My far purpose is to calculate the RTC score for eQTL SNPs. Basically, I have two ideas: 1. Based on the recombination hotspots, the region between two hotspots can be defined as LD intervals, like the intervals used ...
genetics plink ld written 5 months ago by Tao • 300
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Answer: A: How to match alleles for a pair of SNPs using PLINK?
... In pairwise LD calculation of a given SNP pairs, Plink will output the corresponding haplotypes, [see the example here][1]. But it also need to be calculated one pair by one pair. And following scripts would be needed to satisfy my need. [1]: http://zzz.bwh.harvard.edu/plink/ld.shtml ...
written 11 months ago by Tao • 300
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How to match alleles for a pair of SNPs using PLINK?
... Hi, I have a list of variants which are in high LD of a list of GWAS variants. Basically, I want to know the likely risk alleles for proxy variants of a GWAS SNP. For example, we have two SNPs: rsA (A/C) and rsB (T/G), how can I infer the the matching alleles (the most likely haplotype). I would p ...
allele matching plink ld written 11 months ago by Tao • 300
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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 13 months ago by Tao • 300
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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 13 months ago by Tao • 300
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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 13 months ago by Tao • 300
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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 17 months ago by Tao • 300
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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 17 months ago by Tao • 300

Latest awards to Tao

Scholar 12 days ago, created an answer that has been accepted. For A: WGCNA signed vs unsigned network
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Great Question 4 months ago, created a question with more than 5,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 4 months 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 How to tell viruses/bacteria found in human brain Rna-seq samples are intrinsic or contamination?
Popular Question 10 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 11 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 13 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 16 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 16 months ago, created a question with more than 1,000 views. For How to tell viruses/bacteria found in human brain Rna-seq samples are intrinsic or contamination?
Popular Question 17 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Scholar 17 months ago, created an answer that has been accepted. For A: How to choose NCBI viral database?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 20 months ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 2.9 years ago, voted at least 25 times.
Scholar 3.0 years ago, created an answer that has been accepted. For A: How to choose NCBI viral database?
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