User: Tao
Tao • 230
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... 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 10 weeks ago by
Tao • 230
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... 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 ...
written 10 weeks ago by
Tao • 230
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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 4 months ago by
Tao • 230
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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 4 months ago by
Tao • 230
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... 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 4 months ago by
Tao • 230
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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 8 months ago by
Tao • 230
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... 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 8 months ago by
Tao • 230
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... 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 8 months ago by
Tao • 230
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... 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 9 months ago by
Tao • 230
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... 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 9 months ago by
Tao • 230
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