User: serpalma.v

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serpalma.v10
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Germany
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3 hours ago
Joined:
4 years, 7 months ago
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Posts by serpalma.v

<prev • 32 results • page 1 of 4 • next >
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Removing Illumina Single End PCR Primers and TruSeq Adapters
... Dear community I have 1080 FASTQ files and I've run them all through FastQC to evaluate their quality. Then I aggregated the output with the R package fastqcr, which also allowed me to identify distinctingly the sequences found in the module "Overrepresented Sequences". Thus, accross all 1080 file ...
adapter removal dna-seq primer truseq fastqc written 2 days ago by serpalma.v10 • updated 2 days ago by genomax49k
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Recomendations on setting a software pipeline to detect signatures of selection
... Dear community I need to set up a software pipeline to detect signatures of selection between two mouse populations; one has been selected for traitX over the past 4 decades and the other has not been selected and is considered as a control population. Both differ significantly for the trait of int ...
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Differences in RNAseq Variant Calling and Allele Specific Expression
... Dear community Using the GATK's tools "haplotypecaller" and "ASEReadCounter" it is possible to produce a vcf file and a tabulated file for allele specific expression analysis (ASE), respectively. The vcf file contains information about the number of reads mapping to each allele of a heterozygous ...
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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 8 months ago by serpalma.v10 • updated 6 months 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 8 months ago by serpalma.v10 • updated 8 months ago by Pierre Lindenbaum108k
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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 8 months 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 8 months 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 9 months ago by serpalma.v10 • updated 9 months ago by Denise - Open Targets4.5k
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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 10 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 11 months ago by serpalma.v10

Latest awards to serpalma.v

Popular Question 7 months ago, created a question with more than 1,000 views. For Exploratory data anaylsis to detect batch effects
Popular Question 10 months ago, created a question with more than 1,000 views. For Exploratory data anaylsis to detect batch effects
Popular Question 2.2 years ago, created a question with more than 1,000 views. For topGO approach for a list a genes without expression
Popular Question 3.6 years ago, created a question with more than 1,000 views. For topGO approach for a list a genes without expression
Popular Question 3.6 years ago, created a question with more than 1,000 views. For P1 And A Adater Trimming And Mapping From Ion Torrent Reads

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