User: erdiazval

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erdiazval30
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Posts by erdiazval

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Calculating Gene Densities From Rnaseq Data
... I've been working on a similar approach to intersect gene density with cis-variants. 1) get .bam files (GATK's pipeline for SNP calling) and convert them to BED format with bedtools 2) create a genome.bed like-file (chr, length fields) and split it into 1MB chunks with bedtools 3) calculate covera ...
written 5 weeks ago by erdiazval30
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Comment: C: eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer's diseas
... You can use RNA-seq data to mine genetic markers (SNPs & indels) and also to generate expression profiles and perform an eQTL analysis. However, if your are using exon/CDS data, I think your are going to have a very small number of markers in comparison to that you could obtain from whole genome ...
written 4 months ago by erdiazval30
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Answer: A: Tools For Analysis Allele Specific Expression In Rna-Seq Data?
... Hi Sara ASE is a complex task, the pipeline I developed and have being following is this (considering you have both the parental transcriptomes as well as the F1 hybrid transcriptomes: 1) Align parental transcriptomes against the Reference genome (STAR) 2) Call homozygous SNPs with depth > 4 rea ...
written 8 months ago by erdiazval30 • updated 8 months ago by genomax57k
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Answer: A: Extract several fields from vcf file
... I would go for using SNPSift program This is an instance of how I use it to extract: position, ref allele, alt allele, Allele Depth (AD from genotype field), and functional annotation by gene ID. !/bin/bash for i in *.vcf; do java -jar /data/software/snpEff/snpEff/SnpSift.jar\ extra ...
written 8 months ago by erdiazval30
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Answer: A: How to get counts data for allele specific expression analysis (ASE) from aligne
... The first step is to idetifying polymorphisms of your libraries against the reference genome. I would go for a pseudo-reference aproach which implies that you impute the homozygous SNPs of your libraries into the reference genome. Then you align your libraries against both the reference and the pseu ...
written 9 months ago by erdiazval30
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Answer: A: Sleuth: Combined lrt and wt tests, clustered heatmap
... You can use the LTR to test for differential expression and get the log2 foldchange estimates from the kallisto normalized values while you don't include the filtered out values. SNM <- kallisto_table(so, use_filtered = TRUE, normalized = TRUE, include_covariates = TRUE ...
written 10 months ago by erdiazval30

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