User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 7 days ago by harold.smith.tarheel4.5k
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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 5 weeks ago by harold.smith.tarheel4.5k
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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 4 months ago by harold.smith.tarheel4.5k
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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 4 months ago by harold.smith.tarheel4.5k
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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 5 months ago by harold.smith.tarheel4.5k
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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 5 months ago by harold.smith.tarheel4.5k
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Answer: A: Keeping only common variants in the merged VCF file
... Two options: 1) use [BEDtools 'intersect'][1] for the two original VCFs. 2) use [VCFtools 'vcf-annotate'][2] to add the 1000 Genomes rs numbers, then 'grep' to keep the variants that were annotated as such. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html [2]: http ...
written 5 months ago by harold.smith.tarheel4.5k
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Comment: C: Trimmomatic Error : java.lang.ArrayIndexOutOfBoundsException: 1
... Remove the Ns at the beginning of your adapter sequence, rerun the command, and see if that solves your problem. ...
written 8 months ago by harold.smith.tarheel4.5k
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Comment: C: Efficent Estimation of Sequencing Coverage
... [Samtools 'flagstat'][1] outputs the number of mapped reads in your BAM file (plus other metrics). [1]: http://www.htslib.org/doc/samtools.html ...
written 9 months ago by harold.smith.tarheel4.5k
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Answer: A: Efficent Estimation of Sequencing Coverage
... Read length x # of reads x % aligned / size of genome = coverage Coverage scales ~linearly with FASTQ file size (but not gzipped FASTQs), so you can determine the coverage for a few representative files (small/medium/large) and calculate the others based on file size. ...
written 9 months ago by harold.smith.tarheel4.5k

Latest awards to harold.smith.tarheel

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Popular Question 6 weeks ago, created a question with more than 1,000 views. For complex indel precludes detection of overlapping SNPs
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
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
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 21 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 21 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 2.2 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 2.2 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Scholar 2.3 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 2.3 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 2.3 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 2.4 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 2.4 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22

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