User: d-cameron

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d-cameron2.0k
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Australia
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Posts by d-cameron

<prev • 229 results • page 2 of 23 • next >
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Comment: C: What does <*> mean in a vcf file?
... Unfortunately, the specs do not explicitly state whether the symbolic allele includes explicitly listed alt alleles or not. ...
written 6 months ago by d-cameron2.0k
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Comment: C: annotation of SV (structural variants)
... The DELLY authors updated their output to use BND notation (which is good) but they only write one of the two records required for a valid VCF BND breakpoint (which is bad). Technically my tool is doing the correct thing but that isn't particularly useful for users. I have a few other projects taki ...
written 6 months ago by d-cameron2.0k
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Comment: C: NGS data simulation: VarSim or BAMSurgeon?
... Unfortunately not. We do have a benchmarking paper with more comprehensive results coming out soon. ...
written 6 months ago by d-cameron2.0k
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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 11 months ago by d-cameron2.0k
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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 11 months ago by d-cameron2.0k
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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 12 months ago by d-cameron2.0k
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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 12 months ago by d-cameron2.0k
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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 12 months ago by d-cameron2.0k
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Comment: C: How to run IGV
... Run igv.bat from a command prompt to see the error message. ...
written 12 months ago by d-cameron2.0k
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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 12 months ago by d-cameron2.0k

Latest awards to d-cameron

Scholar 5 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 4 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
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: Modernising the FASTQ Format
Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Supporter 6 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 14 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 14 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.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 14 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.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 15 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

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