User: Sam

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Sam2.2k
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Posts by Sam

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Answer: A: How to calculate Polygenic Risk Score from Summary Results with Z-Score only
... You can use the z-score for PRS calculation as long as your target and base are from the same population. ...
written 9 weeks ago by Sam2.2k
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Answer: A: Estimating SNP heritability for related individuals from a SNP array
... You can try using [GCTA GREML-KIN][1] which can take into account of relateship information when calculating the SNP heritability [1]: https://cnsgenomics.com/software/gcta/#Overview ...
written 9 weeks ago by Sam2.2k
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Comment: C: Plink: Understanding LD Clumping vs Pruning
... If I remember correctly, that blog was written with Polygenic Score Analysis in mind where Clumping is preferred. The reason why clumping is preferred in Polygenic Score analysis is that we want to maintain the SNPs that has the strongest signal (lowest p-value). With pruning, the SNPs were randomly ...
written 5 months ago by Sam2.2k
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Comment: C: High Kmer Content in middle of the read
... Maybe just check the number of reads that show this kind of problem. If the number is small, just remove them ...
written 5 months ago by Sam2.2k
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Comment: C: High Kmer Content in middle of the read
... Unfortunately, that's like 3 years ago and I have no memory of that. I think @Ian's answer should most likely be what's happening ...
written 5 months ago by Sam2.2k
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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 6 months 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 6 months 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 18 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 18 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 18 months ago by Sam2.2k

Latest awards to Sam

Appreciated 8 weeks ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Student 5 months ago, asked a question with at least 3 up-votes. For Interpretation Of Differential Exon Usage Results
Great Question 6 months ago, created a question with more than 5,000 views. For Piping Markduplicates
Popular Question 13 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 22 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 22 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 2.2 years ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practic
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Great Question 2.5 years ago, created a question with more than 5,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Merge 4 Fastq Files
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Scholar 3.3 years ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Piping Markduplicates
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Scholar 3.7 years ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Merge 4 Fastq Files
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Scholar 3.8 years ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data

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