User: harold.smith.tarheel
harold.smith.tarheel • 4.3k
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Posts by harold.smith.tarheel
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... 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.tarheel • 4.3k
2
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109
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... [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.tarheel • 4.3k
2
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1
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109
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... 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.tarheel • 4.3k
2
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1
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... From the manual:
> normalization will only be applied if the --fasta-ref option is
> supplied. ...
written 8 weeks ago by
harold.smith.tarheel • 4.3k
0
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... 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.tarheel • 4.3k
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1
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253
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... 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.tarheel • 4.3k
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526
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... 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.tarheel • 4.3k
2
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1
answer
278
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1
answers
... 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.tarheel • 4.3k
0
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1
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253
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... 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.tarheel • 4.3k
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... 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.tarheel • 4.3k
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