User: Sam

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Sam2.1k
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Posts by Sam

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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 9 weeks ago by Sam2.1k
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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 9 weeks ago by Sam2.1k
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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 10 weeks ago by Sam2.1k
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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 10 weeks ago by Sam2.1k
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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 6 months ago by Sam2.1k
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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 9 months ago by Sam2.1k
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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 9 months ago by Sam2.1k
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... You can change that in the plink bim file ...
written 9 months ago by Sam2.1k
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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 9 months ago by Sam2.1k
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Comment: C: calculate p-value for the r pairwise
... 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 9 months ago by Sam2.1k

Latest awards to Sam

Commentator 22 days ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 5 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 6 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 10 months ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
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