User: genomics Newbie

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Posts by genomics Newbie

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NCBI expect value
... If an NCBI sequence match has an e (expect) value of 5e-128 there is little or no chance that your sequence is by chance, correct? My understanding is that if you have an NCBI E (expect) value of 0 then you can expect to see 0 BLAST hits by chance. Therefore, 5e-128 (-114) would presume that the B ...
ncbi expect value written 16 months ago by genomics Newbie30
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Answer: A: NCBI BLAST - downloads to only include taxa (no alignments)
... Will use command line BLAST. ...
written 16 months ago by genomics Newbie30
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NCBI BLAST - downloads to only include taxa (no alignments)
... After performing a NCBI BLAST search I am able to download results in a variety of formats, including text, XML, json, etc. If I download using text format both the taxon results and alignments are shown. I just want to see the results without the associated alignment. What would be the best fo ...
blast written 16 months ago by genomics Newbie30
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Microbiome Taxonomy composition
... Hello, I am doing a microbiome analysis and am trying to gain an understanding of those taxa which did not have at least a phylum or family level assignment. I did a NCBI Blast for about 5 of the "unclassified" taxa and their taxonomy was Influenza Virus A at 100% identity. Any feasible exaplan ...
microbiome taxonomy written 18 months ago by genomics Newbie30 • updated 18 months ago by Carambakaracho2.2k
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RNA-Seq QC for aligned files (bam)
... Hello, I am trying to find a qc package to be used with.bam files. In using the RNA-SeQC package I ran into difficulty because it required -s, -r, and -r arguments. I only have a .bam file and do not have these required parameters. Is there a RNA-Seq specific QC tool where I can simply point ...
bam qc rna-seq written 20 months ago by genomics Newbie30 • updated 20 months ago by Friederike6.4k
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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 24 months ago by genomics Newbie30 • updated 24 months ago by Emily_Ensembl21k
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Comment: C: Using Bioconductor package for gene expression analysis
... The sequences were provided to us in .bam format. ...
written 2.0 years ago by genomics Newbie30
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Comment: C: Using Bioconductor package for gene expression analysis
... We currently have rna-seq sequences in bam format. ...
written 2.0 years ago by genomics Newbie30
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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 2.0 years ago by genomics Newbie30 • updated 2.0 years ago by Charles Warden7.9k
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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 2.2 years ago by genomics Newbie30 • updated 2.2 years ago by Kevin Blighe66k

Latest awards to genomics Newbie

Popular Question 16 months ago, created a question with more than 1,000 views. For hg19 exome reference and index
Scholar 16 months ago, created an answer that has been accepted. For A: NCBI BLAST - downloads to only include taxa (no alignments)
Popular Question 19 months ago, created a question with more than 1,000 views. For hg19 exome reference and index
Popular Question 19 months ago, created a question with more than 1,000 views. For Finding adapters in sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For Convert fastq to plink .bed
Popular Question 20 months ago, created a question with more than 1,000 views. For hg19 exome reference and index
Popular Question 24 months ago, created a question with more than 1,000 views. For Finding adapters in sequences
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Creating a BWA index with an index_prefix

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