User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 12 days ago by harold.smith.tarheel4.4k
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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 16 days ago by harold.smith.tarheel4.4k
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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 weeks ago by harold.smith.tarheel4.4k
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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 weeks ago by harold.smith.tarheel4.4k
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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 8 weeks ago by harold.smith.tarheel4.4k
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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 4 months ago by harold.smith.tarheel4.4k
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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 5 months ago by harold.smith.tarheel4.4k
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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 5 months ago by harold.smith.tarheel4.4k
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Answer: A: bcftools doesn't normalize the vcf file
... From the manual: > normalization will only be applied if the --fasta-ref option is > supplied. ...
written 6 months ago by harold.smith.tarheel4.4k
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Answer: A: Viral vector integration site detection tool
... See [Identification of the sequence insertion site in the genome][1] [1]: https://www.biostars.org/p/225399/ ...
written 6 months ago by harold.smith.tarheel4.4k

Latest awards to harold.smith.tarheel

Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 5 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 12 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
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 17 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 17 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 19 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 19 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 19 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 22 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 22 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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
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
Scholar 2.1 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 2.1 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 2.1 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
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 2.4 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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