User: harold.smith.tarheel

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Posts by harold.smith.tarheel

<prev • 523 results • page 1 of 53 • next >
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Answer: A: Filter only SNPs in 1000 Genomes Data Slicer
... It's probably easiest to filter the VCFs after retrieval. [VCFtools][1] --remove-indels or [vcflib][2] vcfsnps will do the job. [1]: https://vcftools.github.io/man_latest.html#BASIC%20OPTIONS [2]: https://github.com/vcflib/vcflib#vcffilter ...
written 5 weeks ago by harold.smith.tarheel4.6k
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Answer: A: GATK VariantFiltration does not filter
... From the command description: "A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed." In the SNP example you posted, it's annotated as 'PASS' - as it should be. ...
written 4 months ago by harold.smith.tarheel4.6k
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Answer: A: comparison of variants between WGS samples
... [VCFtools][1] '--diff' command can be used to compare VCFs for unique and shared variant calls. [1]: https://vcftools.github.io/index.html ...
written 4 months ago by harold.smith.tarheel4.6k
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Answer: A: Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vc
... [VCFtools][1] '--freq' flag will output allele frequencies; you can then parse those values using 'awk' to replace the genotype call. [1]: https://vcftools.github.io/man_latest.html ...
written 12 months ago by harold.smith.tarheel4.6k
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Answer: A: in bcftools mpileup output, the DP number is not equal to depth in I16 tag
... (note: relying on memory) 1. I believe I16 values comprises only high-quality (>Q13) bases, while the DP value is for all bases. 2. 'mpileup' calculates genotype likelihoods based on the frequency of REF vs ALT bases. To determine the actual variant (including the number of reads used to call th ...
written 13 months ago by harold.smith.tarheel4.6k
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Comment: C: Illumina paired-end reads R1 and R2 mixed together?
... PCR-based methods (as opposed to ligation) will produce directional libraries. You can either incorporate the Illumina adapter sequences into your amplicon primers, or add them via two rounds of PCR (first round with amplicon primers, second round with Illumina adapters + amplicon overhang). ...
written 13 months ago by harold.smith.tarheel4.6k
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Answer: A: Interpreting bbduk histogram headers and contents
... Adding to @h.mon's answers: 2) Minor correction: the top PHRED score is 41 (ASCII character 'J' in Sanger format). 4) The instrument is programmed to sequence +1 cycle relative to the desired read length. This additional nucleotide is used for phasing/prephasing base-call correction. 5) Quality s ...
written 14 months ago by harold.smith.tarheel4.6k
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Answer: A: The same location shares different GeneBank Accession in IGV and UCSC?
... The difference is RNA vs DNA. The histone genes are repetitive. There are four identical copies (plus several nearly identical ones) of this gene in the genome (DNA). The accession numbers you list are RefSeq RNAs for those four copies. So each (identical) RNA maps to multiple loci - and, conversely ...
written 14 months ago by harold.smith.tarheel4.6k
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Comment: C: Comparing calls from different VCFs
... From the [BEDtools 'intersect'][1] documentation: > There will likely be cases where you’d like to know which “A” features > do not overlap with any of the “B” features. Perhaps you’d like to > know which SNPs don’t overlap with any gene annotations. The -v (an > homage to “grep -v”) op ...
written 15 months ago by harold.smith.tarheel4.6k
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Answer: A: Why are there many reads with green color in IGV of RNA-seq data?
... Ribosomal RNA contamination is common for RNA-Seq, and the genes encoding rRNA are tandem repeats.Check to see if that's the reason. ...
written 18 months ago by harold.smith.tarheel4.6k

Latest awards to harold.smith.tarheel

Popular Question 9 days ago, created a question with more than 1,000 views. For How to calculate genetic diversity in inbred population
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What factors impact the total number reads produced by different sequencing inst
Popular Question 7 months ago, created a question with more than 1,000 views. For how to extract unique variants from GVCF
Popular Question 10 months ago, created a question with more than 1,000 views. For complex indel precludes detection of overlapping SNPs
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 14 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 14 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Popular Question 15 months ago, created a question with more than 1,000 views. For complex indel precludes detection of overlapping SNPs
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 23 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 2.9 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 3.1 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 3.3 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal

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