User: Sam
Sam • 2.1k
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Posts by Sam
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... I'd suggest you to perform a partitioning of heritability and see if majority of the heritability lies within these regulatory elements. [LDSC][1] is one of the tool that can perform that
Though the problem of this approach is that it doesn't provide you with a SNP based probability
[1]: https:/ ...
written 7 months ago by
Sam • 2.1k
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Comment:
C: 1000 genomes PCA for whole genome
... You can read [here][1]. Though I do suggest you to follow Kevin's tutorial
[1]: https://www.cog-genomics.org/plink/1.9/input#vcf_filter ...
written 7 months ago by
Sam • 2.1k
1
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Comment:
C: 1000 genomes PCA for whole genome
... As mentioned by GabrielMontenegro, you will need to do the following:
1. clean the multi-allelic sites from your files
2. remove or rename duplicated SNPs
3. perform pruning using either `--indep` or `--indep-pairwise`
4. Extract pruned SNPs with `--extract`
5. perform PCA using `--pca`
(You can ...
written 7 months ago by
Sam • 2.1k
1
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... If your genotype is in vcf format, you can convert it to plink format then use the --pca function from PLINK.
If you have large number of samples (which shouldn't be the case if you are using 1000G), then you can consider [flashPCA][1]
Note: If you are directly converting the vcf to plink format, ...
written 7 months ago by
Sam • 2.1k
2
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1
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Answer:
A: Undrestanding BGEN files
... You can find the detail information of the bgen format here:
http://www.well.ox.ac.uk/~gav/bgen_format/
Basically, this is a type of dosage data.
Unfortunately, the bgen format is in binary. So you will either have to write your own programme or use some external programe to handle them. If all yo ...
written 11 months ago by
Sam • 2.1k
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... Strange. PLINK does not produce empty lines filtered. Maybe you should try and add --geno 0.1 in your plink command to remove SNPs with high missingness? ...
written 14 months ago by
Sam • 2.1k
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... Try to do the following code
sed 's/^chrM\s/25\t/g; s/^chrX\s/23\t/g; s/^chrY\s/24\t/g; s/^chr//g' your.bim > fixed.bim
Should help you to modify the bim file. As for your error, it is likely that your replace has changed the number of line of bim, leading to the problem ...
written 14 months ago by
Sam • 2.1k
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724
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... You can change that in the plink bim file ...
written 14 months ago by
Sam • 2.1k
0
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2
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671
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Comment:
C: gene list annotation
... There are many different tools. To name a few [DAVID][1], [GOrilla][2] will be somewhere to start
[1]: https://david.ncifcrf.gov
[2]: http://cbl-gorilla.cs.technion.ac.il ...
written 14 months ago by
Sam • 2.1k
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1
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... how can you perform a pairwise correlation if you don't have data of equal length? You won't even have the pairwise R, right?
...
written 14 months ago by
Sam • 2.1k
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For C: difference between assembly hg19 and GRCh37
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