User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 2 days ago by harold.smith.tarheel4.2k
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Comment: C: Missing sequence from a cosmid de novo assembly
... Why would you search for the missing sequence in the assembled contigs, when you've already said that it's missing? I recommended aligning your data (i.e., your reads) to the missing sequence. Or, you can parse that data for substrings. ...
written 18 days ago by harold.smith.tarheel4.2k
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Comment: C: Explaining fragment distribution plots from ATAC-seq
... The spikes at 140bp and 150bp correspond to the size of the core nucleosome particle in conjunction with the 10bp periodicity of the DNA helix mentioned by @ATpoint. These sizes were first reported by biochemists Axel, van Holde, Kornberg, and others in the 1970s, using micrococcal nuclease digestio ...
written 19 days ago by harold.smith.tarheel4.2k
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Comment: C: BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
... Your sample has already been filtered (demultiplexed). The point by @michael.ante is that 'grep' matches both the barcode in the header as well as any reads that contain that sequence string. Notice that the value returned by grep (~460M) is larger than the number of reads in your file reported by B ...
written 5 weeks ago by harold.smith.tarheel4.2k
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Answer: A: Missing sequence from a cosmid de novo assembly
... Two easily testable possibilities: 1) Spades failed to assemble the reads for this segment. 2) Reads for this segment are not present in your sample/data. You can discriminate by aligning your data to the sequence in question. ...
written 6 weeks ago by harold.smith.tarheel4.2k
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Comment: C: Low percentage of Illumina reads retained after trimming with Trimmomatic
... The explanation by @JV is correct. The Adapter Content graph before trimming indicates that majority of your inserts are significantly shorter than your read length (some as short as 30bp). This should have been obvious to the bench scientist who assessed the library by TapeStation. @genomax is cor ...
written 6 weeks ago by harold.smith.tarheel4.2k
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Answer: A: Find unique non overlapping intervals between two files?
... Use [BEDtools subtract][1] with -A option. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html?highlight=subtract ...
written 11 weeks ago by harold.smith.tarheel4.2k
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Answer: A: Combining snp and indel vcf files with GATK4
... My guess (easily verified) is that you have some overlapping SNPs and indels that are being merged. I don't know which takes precedence in MergeVcf - v3 CombineVariants allowed the option to specify which one. SortVcf would not resolve overlaps but merely but put them in chromosome/position order, t ...
written 3 months ago by harold.smith.tarheel4.2k
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Comment: C: how to extract unique variants from GVCF
... @Ram: Sorry for the confusion. I thought your comment was directed at me, since I mentioned cross-posting on GATK. I still intend to share Pierre's solution there, so others will be aware of it. ...
written 5 months ago by harold.smith.tarheel4.2k
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Comment: C: how to extract unique variants from GVCF
... Will do. I cross-posted here only b/c the response time there can be... slow. ...
written 5 months ago by harold.smith.tarheel4.2k

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Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
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 11 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 11 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 13 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 13 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 16 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 16 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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
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
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
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
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 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 2.0 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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