User: Mr Locuace

gravatar for Mr Locuace
Mr Locuace100
Reputation:
100
Status:
Trusted
Location:
Chile
Last seen:
2 weeks, 3 days ago
Joined:
4 years, 8 months ago
Email:
l*******@gmail.com

Molecular biologist by training that recently joined a Human Genomics group.

Posts by Mr Locuace

<prev • 65 results • page 1 of 7 • next >
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Get % of identity of a list of human genes with their homologous genes in other species
... I want to compare the % of identity of 100 human genes with their homologous genes in 6 primate species. Ensemble provides very nice tools to visualize sequence alignments between humans and other species but apparently does not provide a quantitative measure of identity for a whole gene. Any sugges ...
alignment sequence written 17 days ago by Mr Locuace100 • updated 17 days ago by genomax87k
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Phases switches in local ancestry inference (LAMP-LD vs RFMix)
... Hello. I am working on the revision of a manuscript were we used LAMP-LD software to infer local ancestry of a SNP dataset. One reviewer made the following comment: "The local ancestry inference program LAMP-LD does not correct for phases switches, which can substantially lower confidence in local ...
rfmix phase switches phasing lamp-ld written 3 months ago by Mr Locuace100
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Comment: C: Find genome coordinates of nucleotide sequence within specific gene
... Amazing ! Thanks so much @Alex Reynolds !! ...
written 3 months ago by Mr Locuace100
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Find genome coordinates of nucleotide sequence within specific gene
... I have a nucleotide sequence "CACTGCC" and I want to know the physical coordinates (start position and end position) of this sequence in a specific gene (all occurrences), let's say NOTCH1. Here there is a Biopython solution that scans the whole genome and retrieves all occurrences of the sequence: ...
fasta physical positions biopython written 3 months ago by Mr Locuace100 • updated 3 months ago by Alex Reynolds30k
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Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
... Great, thanks @vkkodali ! ...
written 7 months ago by Mr Locuace100
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Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
... Thanks very much @vkkodali ! But how to do it for a large list of GeneIDs? ...
written 7 months ago by Mr Locuace100
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Retrieve genomic physical coordinates of 3'UTR for set of genes
... Hello, I have a list of human genes and I'd like to retrieve the physical coordinates (GRCh37/hg19 assembly) of their 3'UTRs. Are you aware of any software that can do that? Thanks ! ...
3'utr written 7 months ago by Mr Locuace100 • updated 7 months ago by vkkodali2.0k
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Find gene affected by specific regulatory region
... I have some some SNPs mapping regulatory elements (TFBS, enhancer, promoter-flanking region) that are 72 -45 Kb away from a particular gene A. I want to know if there is a bioinformatic tool that predicts whether such elements affect the transcription of gene A. Thanks ! ...
regulation promoter enhancer snp written 8 months ago by Mr Locuace100
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Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
... Thank you very much @ATpoint ! ...
written 12 months ago by Mr Locuace100
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Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
... Thank you @Sean Davis !. But what about the single file that says "PAIRED"?. How to know if it is actually single-end or a merge between read1 and read2 paired-ends? ...
written 12 months ago by Mr Locuace100

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Popular Question 6 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 6 months ago, created a question with more than 1,000 views. For Plink. How to create small .ped file from big .ped file?
Popular Question 6 months ago, created a question with more than 1,000 views. For Plink. Convert ped files of artificially mixed population into vcf using recode
Popular Question 7 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
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Popular Question 17 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
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Popular Question 23 months ago, created a question with more than 1,000 views. For Lift over based on physical position from GRCh37 build 137 to GRCh37 build 132
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