User: Jautis

gravatar for Jautis
Jautis300
Reputation:
300
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Trusted
Location:
United States
Last seen:
3 weeks ago
Joined:
6 years ago
Email:
t***@duke.edu

Posts by Jautis

<prev • 108 results • page 1 of 11 • next >
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Comment: C: Calculating Tajima's D from SNP frequency data
... I don't think it's possible from this summarized data. Tajima's D is calculated within a population and requires knowing the number of pairwise differentiated sites between individuals. ...
written 5 weeks ago by Jautis300
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Comment: C: A strange R limma voom function mean-variance trend
... OP, did you ever figure this out? I see something similar if I don't filter out lowly expressed genes but do still see a strong positive relationship after doing so ...
written 6 weeks ago by Jautis300
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Answer: A: 012 genotype matrix using vcf tools
... The 012 output is n-by-features, rather than features-by-n. That means that each row is an individual and each column is a snp. ...
written 12 weeks ago by Jautis300
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GO based on NCBI annotation
... Hello, I have RNAseq data for a non-model organism whose genome has been annotated by NCBI but not ensembl. I've been looking at methods for GO/GSEA but they all seem to rely upon ensembl gene IDs and annotations. Are there any similar options using NCBI annotations gene ids or db_xref labels? T ...
genome enrichment gsea go written 6 months ago by Jautis300
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Comment: C: Phasing non-human genomes with Beagle - do I need to divide subjects by populati
... Did you find the answer to this? I'm looking for the same bit of information ...
written 7 months ago by Jautis300
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Comment: C: How to remove a list of reads from fastq file?
... Hello, I'm trying this but (i) the quality score information isn't be returned and (ii) the '@' from the read name line is missing. Looking at the script, I can't figure out why this would be -- think you can help update it again? ...
written 8 months ago by Jautis300
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find position of snps in cM, given recombination map from ldhelmet
... Hello, I have a recombination map calculated from LDhelmet which has estimates of recombination rates for windows of the genome (in recombination events per generation per bp) and a separate file of SNP locations which I would like to transform from base number to location in centiMorgans. Is there ...
genome recombination physical position written 11 months ago by Jautis300
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Convert VCF + LDhelmet Recombination Rates to EIGENSTRAT format
... Hello, I have a vcf file of called variants (GATK) and genotypes per individual and a text file produced from LDhelmet which contains recombination rates for windows across the genome (4 columns: chromosome, start, end, and recombination rate). I'm looking to convert this to [the eigenstrat format]( ...
vcf linkage snp genome written 12 months ago by Jautis300
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Comment: C: sed (or similar) command to remove part of the FORMAT from a vcf file?
... Awesome, thank you! I didn't know bcf would get rid of tags in addition to writing new ones ...
written 12 months ago by Jautis300
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sed (or similar) command to remove part of the FORMAT from a vcf file?
... Hello, I'm looking for a quick way to remove PGT, PID, and PS from the FORMAT of a vcf file output by GATK. Currently, some sites have these flags while others don't (see example below). For downstream processing in another program, I need all sites to have the same flags and phasing information doe ...
vcf processing sed written 12 months ago by Jautis300 • updated 12 months ago by finswimmer14k

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Check for Msp1 digestion in sequencing data
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Check for Msp1 digestion in sequencing data
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