User: Alice

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Alice230
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USA
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bio_alice
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12 hours ago
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Posts by Alice

<prev • 63 results • page 1 of 7 • next >
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Comment: C: VCF SNP analysis
... You can start with this guide from GATK people: https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it ...
written 10 days ago by Alice230
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Using GFF3Writer in Biopython
... Hi all, I am having trouble figuring out `GFF3Writer` tool from `Biopython`. I have a regular ensembl `gff3` file and want to extract only certain types of features. I get an empty gff output with only one header line. What am I doing wrong? Here is my code below.: ``` in_file = "test.gff ...
gff3 ensembl gff biopython written 11 days ago by Alice230 • updated 11 days ago by finswimmer2.1k
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Comment: C: Select union of multiple-sample VCF
... GATK has "combine variants" tool: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php ...
written 29 days ago by Alice230
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Answer: C: Filtering a vcf based on known variants
... What are your file formats? You can use bedtools to intersect variants with coordinates, it can work with both -bed and -vcf files. ...
written 4 weeks ago by Alice230
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Comment: C: How to check if BAM is indel-realigned?
... yay it worked! thanks ...
written 4 weeks ago by Alice230
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Comment: C: Difference between Allele frequency spectrum and Joint allele frequency spectrum
... My explanation is very simplified, I just made it to be intuitive. Furthermore, I guess these numbers may be log-transformed for plotting, and I don't remember exactly what they did for these figures. AFS is estimated from allele counts, i.e. how many times you see a SNP in a population. 20 chromo ...
written 4 weeks ago by Alice230
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How to check if BAM is indel-realigned?
... I have a few BAM files from collaborators and I do not know if these were indel-realigned. People who was working on these files are no longer working in the lab, so I have no sources of information about details of these alignments. Is there a way to check if these files were indel-realigned? ...
gatk bam alignment indel-realignment written 4 weeks ago by Alice230
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Answer: A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
... Joint allele frequency spectrum is allele frequency distribution calculated between two\three populations. Imagine a 2D plot, where on x axis is AFS of population 1 and on y axis is AFS in population 2. For example, you can plot derived allele counts in Yoruba versus Central European population. Le ...
written 4 weeks ago by Alice230
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Simulate genotype likelihoods
... I am looking for a package to simulate genotype likelihoods using a vcf file. Something similar to ANGSD tool http://popgen.dk/angsd/index.php/MsToGlf But instead of msms input, I have simulated vcf files. I was thinking to simulate reads (using the vcf) and then call genotypes and GL. But maybe th ...
variant calling vcf snp written 4 months ago by Alice230 • updated 3 months ago by Biostar ♦♦ 20
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Answer: A: Completely confused about terminology and what I'm actually analysing here
... 1) some of them probably are, some are probably not, if these are published, all info should be in the paper; 2) I am not an RNA person, but any aligner, such as bwa, should work; 3) I guess it depends on your data and goals of the project. You probably should get some theoretical knowledge in RNA ...
written 6 months ago by Alice230

Latest awards to Alice

Scholar 24 days ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Scholar 4 weeks ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Popular Question 3 months ago, created a question with more than 1,000 views. For Compare samples in one multisample VCF file
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Great Question 24 months ago, created a question with more than 5,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 24 months ago, created a question with more than 1,000 views. For What Does A Likelihood Ratio Test Of 0 Mean? ( R:Phylosig {Phytools}. P-Value=0)?
Popular Question 24 months ago, created a question with more than 1,000 views. For Need Advice On Performing Bayesian Model Selection Using The Mrbayes Tool.
Popular Question 24 months ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Need Advice On Performing Bayesian Model Selection Using The Mrbayes Tool.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.9 years ago, created a question with more than 1,000 views. For K-Mer Counting From Single-End, Paired-End And Mate-Pair Reads
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