User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 6 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 8 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 8 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 8 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 9 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 10 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 13 months ago by harold.smith.tarheel4.6k
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Answer: A: targets in a bed at or above a coverage
... BEDtools will get you 90% there: bedtools genomecov -ibam FILE.BAM -bg | awk '$4 > 249' > OUTPUT.BG bedtools intersect -a TARGET.BED -b OUTPUT.BG -wao > OVERLAP The first command reports the regions in your BAM with the desired coverage, the second reports the number of basepairs ...
written 13 months ago by harold.smith.tarheel4.6k
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Comment: C: NGS Data storage solutions for small organisations or big labs
... You'd be surprised how easy it is. 40K+ clones (two whole-genome RNAi libraries for *C. elegans*) fit in a couple freezer racks, and we retrieve samples from those regularly (much more frequently than cold datasets). ...
written 14 months ago by harold.smith.tarheel4.6k
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Answer: A: NGS Data storage solutions for small organisations or big labs
... My decidedly heterodox position (probably due to my foundational training in molecular biology) is to store the 'cold' data as library DNA in a -80˚ freezer. DNA is a technologically stable and incredibly information-dense platform - a small freezer could easily accommodate petabytes-to-exabytes equ ...
written 14 months ago by harold.smith.tarheel4.6k

Latest awards to harold.smith.tarheel

Teacher 4 weeks 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 11 weeks ago, created a question with more than 1,000 views. For how to extract unique variants from GVCF
Popular Question 5 months ago, created a question with more than 1,000 views. For complex indel precludes detection of overlapping SNPs
Scholar 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 9 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Popular Question 10 months ago, created a question with more than 1,000 views. For complex indel precludes detection of overlapping SNPs
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 18 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 2.1 years ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 2.5 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 2.5 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 2.7 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 2.7 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 2.7 years ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
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
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30

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