User: Sam

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Sam2.2k
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Posts by Sam

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Answer: A: Base file of PRSice software
... The base file is a GWAS association file. Usually you can obtain it from external data base (e.g. PGC). For Type 2 Diabetes, you might be able to get the summary statistics from WTCCC. Alternatively, if you have an independent data set (independent to your target data), you can also perform the GWAS ...
written 5 weeks ago by Sam2.2k
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Answer: A: PRSice: Imputation and clumping
... The thing is, we only perform clumping on SNPs that were found in both the target and base file. By using the imputed data, you increase the coverage and might result in more post-clumped SNPs, therefore increase amount of information and possibly increase the performance of your PRS model ...
written 5 weeks ago by Sam2.2k
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Answer: A: GWAS: How to estimate probability of SNP association being result of one specifi
... 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 13 months ago by Sam2.2k
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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 13 months ago by Sam2.2k
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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 13 months ago by Sam2.2k
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Answer: A: 1000 genomes PCA for whole genome
... 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 13 months ago by Sam2.2k
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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 17 months ago by Sam2.2k
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... 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 20 months ago by Sam2.2k
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... 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 20 months ago by Sam2.2k
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... You can change that in the plink bim file ...
written 20 months ago by Sam2.2k

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Popular Question 8 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
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Popular Question 17 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 21 months ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis
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