User: eurioste

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eurioste20
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Posts by eurioste

<prev • 10 results • page 1 of 1 • next >
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Assessing mapping quality from BAM files
... I have obtained multiple bam files mapped with BWA. I wish to asses if the mapping of my reads was successful and will give me useful data for a ChIP-seq experiment. Because this is a pilot experiment, I have **no technical duplicates**, just the input and one file for each ChIP protein/histone modi ...
bam chip-seq mapping written 22 months ago by eurioste20 • updated 22 months ago by Hussain Ather940
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Comment: C: Correct way of merging samples for father, mother, child trio variant calling
... Sorry, I wasn't aware this was a bad practice, but, why could it annoy someone? ...
written 2.4 years ago by eurioste20
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Comment: C: Correct way of merging samples for father, mother, child trio variant calling
... Just to make sure I got it right, should I merge the bam files after the the alignment to reference step using samtools mpileup? ...
written 2.4 years ago by eurioste20
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Correct way of merging samples for father, mother, child trio variant calling
... I am new to NGS data analysis and I'm working in a multiple-sample variant calling workflow. I have Illumina-Miseq fastq files (paired end, raw reads) for a father, mother and child trio, one pair for each individual, totalling 6 files. I could trim, align, do the pre-processing and variant calling ...
vcf variant calling bam written 2.4 years ago by eurioste20 • updated 2.4 years ago by Pierre Lindenbaum124k
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Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
... My final objective is to get the "Minor Allele Frequencies" (MAF) for all the 1000 Genomes SNPs (in H. sapiens GRCh37 in case you ask). **I specifically need to obtain data referent to the low coverage Phase 1** of the project, as I require unbiased low coverage data for a machine learning model. ...
maf 1000genomes vep vcf2maf ensembl written 2.4 years ago by eurioste20 • updated 14 months ago by zx87548.4k
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Getting 1000 Genomes phase one MAF values
... I need to get the global 1000 genomes phase 1 minor allele frequencies for all 1000 Genomes low coverage phase 1 SNPs. I have the 1000 genomes .vcf files. Which is the easiest way to get this values? Any suggested tool? ...
maf 1000 genomes written 2.4 years ago by eurioste20 • updated 2.2 years ago by Cyriac Kandoth5.4k
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MCS-R2 (encode HS-40) hg19 genomic coordinates
... This should be easy but I'm trying without success to get the specific hg19 genomic coordinates to a DNase hypersensitivity region named HS-40, also known as MCS-R2, present on chromosome 16 and known to be of importance to the regulation of alpha-globin, but I can't find on papers any reference to ...
assembly dnase encode coordinates written 2.8 years ago by eurioste20
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Comment: C: Gene Set Enrichment Analisys on Bioconductor?
... I am interested in comparing the gene sets of different epigenetic markers to see if they are similar among themselves, in other words, if the genes that had mark A are the same that had mark B. Not all of my gene sets are that big but some marks like H3K36me3 are quite common. ...
written 3.0 years ago by eurioste20
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Gene Set Enrichment Analisys on Bioconductor?
... I'm just a beginner with gene set enrichment analysis, so if I'm making any mistake please let me know. I'm working with a model for predicting functional effect some no coding variants. I simulated all the possible SNVs genome wide. Them I selected the variants scored by the model above a certain ...
gene R jaccard enrichment written 3.0 years ago by eurioste20 • updated 3.0 years ago by Guangchuang Yu2.3k
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Conservation of SNPs contexts
... I'm currently working in a model for differentiating some kinds of SNPs according to genomic signatures presen is their contexts. One of the such signatures is wether the genomic context is conserved among primates (Pan, Pongo, Gorilla, etc).   There are many kinds of different conservation measur ...
conservation genome mutation snp written 5.5 years ago by eurioste20

Latest awards to eurioste

Student 2.4 years ago, asked a question with at least 3 up-votes. For Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs

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