User: Tao
Tao • 350
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... Hi, I got the same problem. That is because when you were converting plink to vcf, probably using plink --recode vcf, "The A2 allele is saved as the reference and normally flagged as not based on a real reference genome ('PR' INFO field value)." See plink explanation [here][1]. That's saying the --r ...
written 4 months ago by
Tao • 350
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... 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 ...
written 6 months ago by
Tao • 350
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... 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 6 months ago by
Tao • 350
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... 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 ...
written 11 months ago by
Tao • 350
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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 17 months ago by
Tao • 350
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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 17 months ago by
Tao • 350
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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 19 months ago by
Tao • 350
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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 19 months ago by
Tao • 350
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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 19 months ago by
Tao • 350
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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 23 months ago by
Tao • 350
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