User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 16 days ago by harold.smith.tarheel4.3k
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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 weeks ago by harold.smith.tarheel4.3k
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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 weeks ago by harold.smith.tarheel4.3k
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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 8 weeks ago by harold.smith.tarheel4.3k
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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 8 weeks ago by harold.smith.tarheel4.3k
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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 11 weeks ago by harold.smith.tarheel4.3k
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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 11 weeks ago by harold.smith.tarheel4.3k
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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 3 months ago by harold.smith.tarheel4.3k
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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 3 months ago by harold.smith.tarheel4.3k
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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 3 months ago by harold.smith.tarheel4.3k

Latest awards to harold.smith.tarheel

Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Scholar 5 weeks 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 8 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
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 15 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 15 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
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
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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
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
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
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
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
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 2.1 years ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 2.2 years ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30

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