User: genomics Newbie

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Posts by genomics Newbie

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Ensembl Data Slicer
... [Ensembl Data Slicer][1] [1]: http://grch37.ensembl.org/Homo_sapiens/Tools/DataSlicer Ensembl (the URL above) provides a feature where one can create a vcf with sample populations (i.e. YRI) from 1000 genomes. It appears to be restricted to a region within a single chromosome. Any idea of how ...
data slicer ensembl 1000 genomes populations written 5 weeks ago by genomics Newbie10 • updated 5 weeks ago by Emily_Ensembl16k
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Comment: C: Using Bioconductor package for gene expression analysis
... The sequences were provided to us in .bam format. ...
written 9 weeks ago by genomics Newbie10
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Comment: C: Using Bioconductor package for gene expression analysis
... We currently have rna-seq sequences in bam format. ...
written 9 weeks ago by genomics Newbie10
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Using Bioconductor package for gene expression analysis
... We have RNA-Seq sequences in bam format and would like to perform gene expression analysis for specific genes. The most important step for us is to prepare count matrices. Questions… 1. Is Bioconductor’s rnaseqGene the best tool to use for gene expression with RNA-Seq sequences? It appears to e ...
gene expression rna-seq written 9 weeks ago by genomics Newbie10 • updated 9 weeks ago by Charles Warden5.8k
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vcf filter of lowQual
... How do I filter my vcf so that all "lowQual" entries are excluded from the variant file. When I ran the following command I included the -e flag which I thought would exclude all LowQual, but they appear in my vcf and I need to remove them so that I can use my vcf as further input into another pi ...
vcf filter written 4 months ago by genomics Newbie10 • updated 4 months ago by Kevin Blighe33k
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plink .bim file missing variant ID
... Hello, First I generated a pileup from my BAM sequences and converted the pileup to vcf. samtools mpileup -uf ucsc.hg19.fasta sample_rna-seq.bam | bcftools call -mv -Oz > calls.vcf.gz I then used PLINK to make the bed, bim and fam files. Although the format was correct, the Variant ID was mi ...
.bim plink snp written 4 months ago by genomics Newbie10
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(Closed) convert .bed (uscs) format to .bed (plink) format
... Hello. Is it possible to convert a .ucsc .bed format to a plink .bed format without routing it through a .vcf? ...
.bed formats written 4 months ago by genomics Newbie10 • updated 4 months ago by Devon Ryan86k
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bam to vcf to .bed
... Is the following the correct process? I do not believe I can "convert" .bam to .bed directly. I am converting .bam to vcf using bcftools, and then using plink to prepare .bed and .fam files. bed to vcf using bcftools vcf to bed using plink bed + fam using plink Thank you. ...
vcf bed bam written 5 months ago by genomics Newbie10 • updated 5 months ago by finswimmer8.0k
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Comment: C: Merging individual .bed files?
... SNP genotype analysis ...
written 5 months ago by genomics Newbie10
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Merging individual .bed files?
... Hello, Our main goal is to create a single set of .bed/.bim/.fam files from our .bam formatted sequences. However I’m finding that merging, sorting and indexing these .bam files (appox. 100) via samtools is exceeding our processing and storage capabilities. 1). Is there any other means by whic ...
.bam .bed samtools .bamtobed written 5 months ago by genomics Newbie10

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