User: Alice

gravatar for Alice
Alice250
Reputation:
250
Status:
Trusted
Location:
USA
Twitter:
bio_alice
Last seen:
5 days, 14 hours ago
Joined:
5 years, 8 months ago
Email:
p*************@yahoo.com

Posts by Alice

<prev • 67 results • page 1 of 7 • next >
2
votes
1
answer
102
views
1
answer
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 12 days ago by Alice250 • updated 12 days ago by bernatgel1.3k
0
votes
0
answers
93
views
0
answers
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 12 days ago by Alice250
1
vote
1
answer
110
views
1
answers
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 12 days ago by Alice250
1
vote
2
answers
149
views
2
answers
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 16 days ago by Alice250
0
votes
0
answers
270
views
0
answers
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 5 months ago by Alice250
1
vote
1
answer
196
views
1
answer
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 5 months ago by Alice250 • updated 5 months ago by finswimmer6.2k
0
votes
0
answers
201
views
0
answers
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 5 months ago by Alice250
3
votes
1
answer
261
views
1
answers
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 5 months ago by Alice250
0
votes
1
answer
285
views
1
answers
Comment: C: How to check if BAM is indel-realigned?
... yay it worked! thanks ...
written 5 months ago by Alice250
1
vote
1
answer
348
views
1
answers
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 5 months ago by Alice250

Latest awards to Alice

Scholar 5 months ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Scholar 5 months ago, created an answer that has been accepted. For A: Difference between Allele frequency spectrum and Joint allele frequency spectrum
Popular Question 8 months ago, created a question with more than 1,000 views. For Compare samples in one multisample VCF file
Supporter 12 months ago, voted at least 25 times.
Great Question 2.4 years ago, created a question with more than 5,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 2.4 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 2.4 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 2.4 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 3.5 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 3.7 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 4.3 years ago, created a question with more than 1,000 views. For Clip Adapters In Sanger Sequencing Traces
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Concatenate Two .Fasta Files Into One
Popular Question 4.3 years ago, created a question with more than 1,000 views. For K-Mer Counting From Single-End, Paired-End And Mate-Pair Reads
Autobiographer 4.8 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1918 users visited in the last hour