User: Alice

gravatar for Alice
Alice260
Reputation:
260
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Location:
USA
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bio_alice
Last seen:
1 week, 3 days ago
Joined:
5 years, 11 months ago
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p*************@yahoo.com

Posts by Alice

<prev • 67 results • page 1 of 7 • next >
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How to convert mutation position from gene coordinate to genome coordinate?
... I have a list of mutations coded as: GENE: c.1234 How do I convert to CHROM: g.1245364? Is there a way, for example, to look them up in genome browser? I played with it a little bit, but could not find gene coordinate option. Thanks in advance. ...
snp coordinate written 3 months ago by Alice260 • updated 3 months ago by bernatgel1.5k
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Comment: C: Should I replace heterozygous variants to make a consensus
... if you want to save information about heterozygosity, you can use IUPAC codes to represent diploid state. ...
written 3 months ago by Alice260
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Answer: C: How to merge two haploid samples (vcf, or g.vcf) into a pseudo-diploid?
... if you have alignments, you can merge 2 BAMs and call genotypes as if like BAM is now diploid. Otherwise I do not think there is a straightforward way to do this. You basically need to recalculate the entire vcf. ...
written 3 months ago by Alice260
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Comment: C: Extract a subset of fasta file based on header in python
... You can try this: - rename 1,2,3 to Contig1, contig2, contig3 (using awk) - samtools index file.fasta, - xargs samtools faidx fasta.file < contigs.txt >> output.fasta ...
written 3 months ago by Alice260
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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 8 months ago by Alice260
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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 8 months ago by Alice260 • updated 8 months ago by finswimmer8.9k
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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 8 months ago by Alice260
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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 9 months ago by Alice260
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Comment: C: How to check if BAM is indel-realigned?
... yay it worked! thanks ...
written 9 months ago by Alice260
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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 9 months ago by Alice260

Latest awards to Alice

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Compare samples in one multisample VCF file
Scholar 8 months ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Scholar 9 months ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Popular Question 11 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 2.6 years ago, created a question with more than 5,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 2.6 years 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 2.6 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 2.6 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.7 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 3.9 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 4.6 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 4.6 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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