User: sbombin

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sbombin10
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1 year ago
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4 years, 5 months ago
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s******@crimson.ua.edu

Posts by sbombin

<prev • 8 results • page 1 of 1 • next >
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How to limit sequences downloaded from NCBI to published data only
... I want to download reference sequences of 28S from NCBI for taxonomic identification of my data. I know that I need to use "Entrez ESearch" to download data. However, I cannot find a way to limit the downloaded data to sequences that have been published in the past. The meta data for sequences that ...
ncbi next-gen esearch reference sequences written 14 months ago by sbombin10
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USEARCH v11alpha_div_rare and -otutab_octave commands
... Does USEARCH version 11 support alpha_div_rare command? it works in v10 but not in v11 for me. Does anyone have the same problem? Also, -otutab_octave command output Fatal Error "prestonsvg2.cpp(91) assert failed: SIZE(Fields) == 3" or "uncross2.cpp(16) assert failed: Freq > 0.0f" depending on t ...
usearch otu miseq metabarcoding written 14 months ago by sbombin10
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GATK RNA-seq best practices
... Hello, I am using GATK Calling variants in RNAseq: http://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq I cannot understand will the expression level will affect the total number of variants found in treatment groups. So for example, if some treatment elevated overa ...
gatk gene expression rna-seq variants written 3.8 years ago by sbombin10 • updated 3.8 years ago by Devon Ryan96k
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Answer: A: Allele specific analysis
... AlleleSeq could perform analysis of allele-specific expression and binding in a network http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208341/ ...
written 3.9 years ago by sbombin10
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Answer: A: Using SnpEff to extract relevant fields
... Hi, I had the same problem. Actually to filter your annotated VCF file based on impact like "High" impact for example, you need to run: java -jar SnpSift.jar filter "ANN[0].IMPACT has 'HIGH'" input_annot.vcf > output_annot_filtered.vcf ...
written 4.1 years ago by sbombin10
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Comment: A: Preparing a .genome file for snpEff
... Hi, If you are working from command line, try to use "/" instead of \ ...
written 4.2 years ago by sbombin10
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RNA-seq SNP analysis
... Hello, I generated VCF and .bam files from transcriptomes files of C.remanei. Now, I want to do some functional annotation of SNPs or some other analyses to begin with. I am actually very new to all these analyses and not sure what is the best way start with. I found some publications with usinf GW ...
variance rna-seq snp functional annotation written 4.2 years ago by sbombin10 • updated 4.2 years ago by Charles Warden7.8k
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Estimate allelic imbalance
... Hello, I am trying to estimate allelic imbalance in C.remanei. Most of the methods that I found require to have separate maternal and paternal transcriptoms to estimate allilic imbalance based on SNPs. However, I have only one combined paternal transcriptom. Does anyone know how to estimate allelic ...
alleles imbalance rna-seq transcriptome written 4.4 years ago by sbombin10

Latest awards to sbombin

Popular Question 3.6 years ago, created a question with more than 1,000 views. For GATK RNA-seq best practices
Popular Question 3.6 years ago, created a question with more than 1,000 views. For RNA-seq SNP analysis

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