User: d-cameron

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d-cameron1.9k
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Posts by d-cameron

<prev • 216 results • page 1 of 22 • next >
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Comment: C: Assembling a sequence from the pairs of letters (X,Y)
... > gns <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) genes(hg19) returns some really strange results. You'll want to use transcripts() instead as some genes are annotated have two transcripts 100+Mb apart so genes() matches almost the whole chromosome for those. The clinical pipelines I'm invol ...
written 6 weeks ago by d-cameron1.9k
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Answer: A: Create a File format to store Variant
... This question is actually very well timed. The GAG4H file formats working group has an upcoming teleconference on the future of VCF and a potential new file format. I strongly recommend getting involved if there are limitations in the existing file formats that make it unsuitable for your use case. ...
written 8 weeks ago by d-cameron1.9k
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Comment: C: sortsam (picard) error in identifyting samfile
... You have redirected the bwa standard error output stream (stderr) to the same location as the standard output stream (stdout. Check your bwa command as redirects such as `2>&1` will do this. Check your shell configuration as well as some configurations will perform this redirect automaticall ...
written 9 weeks ago by d-cameron1.9k
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Comment: C: Does BWA mem ever discard or modify data
... No matter what compressed storage format you use, the majority of the entropy in sequence data is actually in base quality scores, not the actual sequences. If you want 50%+ improvement over fq.gz then you'll be forced to discard information - base quality score binning will make a bigger difference ...
written 9 weeks ago by d-cameron1.9k
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Comment: C: Does BWA mem ever discard or modify data
... >it can clip bases, you'll want to relax the defaults The bases are soft clipped so the information is still there. Only supplementary alignments are hard clipped but the information is in the primary alignment anyway. >reads could also be filtered if they don't map to the reference genome ...
written 9 weeks ago by d-cameron1.9k
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Comment: C: How to run IGV
... Run igv.bat from a command prompt to see the error message. ...
written 9 weeks ago by d-cameron1.9k
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Comment: C: bowtie2 paired end insertion length
... I just use -X 1000 so it works on practically all input libraries. Aren't you getting fewer concordantly alignment reads now? Check the documentation on your simulator (and run picard CollectionInsertSizeMetrics) to see what fragment lengths you've actually simulated. The community can't agree on w ...
written 9 weeks ago by d-cameron1.9k
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Comment: C: bowtie2 paired end insertion length
... Unless you've given a custom -X parameter to bowtie2, fragments longer than 500bp are going to be considered discordant. ...
written 9 weeks ago by d-cameron1.9k
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Answer: A: bowtie2 paired end insertion length
... > See one of my alignment information as below, although it has 100% overall alignment, what is wrong with '1670714 (97.50%) aligned concordantly 0 times'? Nothing is wrong per se, it's just a combination of bowtie2 incorrectly placed at least one of the reads and/or the fragment size being unus ...
written 9 weeks ago by d-cameron1.9k
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Answer: A: assembling a sequence from the pairs of letters (X,Y)
... > what is the optimal strategy to connect these pairs of letters into a sequence Typically assembler are looking for a [Eulerian path][1], Hamiltonian cycle, or a variation of one of those approaches. [1]: https://en.wikipedia.org/wiki/Eulerian_path ...
written 9 weeks ago by d-cameron1.9k

Latest awards to d-cameron

Scholar 9 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 3 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 3 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 3 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
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Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 5 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
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Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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