User: serpalma.v

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serpalma.v10
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New User
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Germany
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3 weeks, 2 days ago
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4 years ago
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Posts by serpalma.v

<prev • 29 results • page 1 of 3 • next >
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Calling ASE using QuASAR without availble population allele frequency
... I am trying to estimate gene level Allele Specific Expression (ASE) within each sample using QuASAR https://www.ncbi.nlm.nih.gov/pubmed/25480375. I have RNAseq data from cows and for each animal I've produced vcfs with HaplotypeCaller (GATK) QuASAR requires as input a file containing the followin ...
vcf maf allele specific expression snp written 7 weeks ago by serpalma.v10 • updated 5 days ago by Biostar ♦♦ 20
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How to find unique mappability regions in the bovine genome?
... From a list of SNPs I want to keep the ones found in unique mappability regions. For human data that is possible to do with the wgEncodeCrgMapabilityAlign100-mer track, but for bovine I cannot find an analogous data base. If there is such information available for bovine, I would greatly appreciate ...
assembly cow snp written 7 weeks ago by serpalma.v10 • updated 7 weeks ago by Pierre Lindenbaum102k
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Answer: A: WASP criterion for discarding reads in unphased samples
... I read the the description of the wasp function filter_remapped_reads.py, the one that comes after remapping the synthetic reads. It says that even if one read of the the synthetic read set matches to a different location than the original read, that original read is discarded. The function uses 3 ...
written 9 weeks ago by serpalma.v10
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WASP criterion for discarding reads in unphased samples
... Dear community I am trying to minimize mapping bias by using WASP http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3582.html. The algorithm first intersects a BAM/SAM file with a VCF file containing the reference SNPs for the species. The original BAM/SAM file is then split into intersecting ...
wasp allele-specific expression rna-seq written 9 weeks ago by serpalma.v10
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SNP annotated outside gene location (Variant Effect Predictor)
... I have the following SNP annotated with variant effect predictor to two genes, their locations in the genome are shown as well (UMD3.1): - rs469441731: chr1:83,591,886-83,591,886 - ENSBTAG00000020106: chr1: 83,583,028-83,591,912 (reverse strand) - ENSBTAG00000019336: chr1: 83,595,844-83,609,419 ...
ensembl vep snp variant effect predictor written 3 months ago by serpalma.v10 • updated 3 months ago by Denise - Open Targets4.1k
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Comment: C: How to find the self aligned repeat region in human genome
... Is there any similar data set for Bos taurus (UMD3.1)?. I've browsed UCSC and Ensembl corresponding directories. ...
written 4 months ago by serpalma.v10
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Comment: C: Feasible Annotation of 4 million unique SNPs
... Thank you Emily, besides the long time to complete the job, is there another negative aspect to run such many variants with the online tool? ...
written 5 months ago by serpalma.v10
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Comment: C: Feasible Annotation of 4 million unique SNPs
... Thank you very much Maxime, the annotations were finished overnight with ensembl tool VEP. I will keep ANNOVAR in mind nevertheless for the future. ...
written 5 months ago by serpalma.v10
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Feasible Annotation of 4 million unique SNPs
... I ran the GATK tool ASEReadCounter to measure allele specific expression (ASE). There were 100 BAM input files processeced by ASEReadCounter. The output (ASE file) is a table for each input file with read counts for the reference allele and the alternative allele (SNP). However, there are no annota ...
gatk ase snp written 5 months ago by serpalma.v10 • updated 5 months ago by Emily_Ensembl14k
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Chromosome Names in genome are incompatible with annotations
... Dear community, while creating an index for the bovine genome with STAR, the process fails because the chromosome names in the annotation file (Bos_taurus.UMD3.1.87.gtf) are incompatible with the ones in the reference file (UMD3.1_chromosomes.fa) (e.g. for chromosome "10" vs "gnl|UMD3.1|GK000010.2 ...
alignment star written 8 months ago by serpalma.v10

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