User: d-cameron

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d-cameron2.2k
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Posts by d-cameron

<prev • 264 results • page 1 of 27 • next >
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Comment: C: Revert bam to fastq
... Write failures are usually either network issues or disk space issues. Is your disk full or disk quota limit reached? ...
written 24 days ago by d-cameron2.2k
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Comment: A: what the mean of Genomic content
... Are you sure "GC" means "genomic content"? GC content typically refers to the predicted nucleotide composition of the genome. That is, how many of the bases are guanosine/cytidine and is expressed as a % of the genome. There is a very real GC-bias in sequencing: sequences that are AT rich or GC rich ...
written 5 weeks ago by d-cameron2.2k
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Answer: A: Is it possible to compute the Loss of heterocigosity from the Copy number variat
... If the copy number does allele-specific copy number calling then yes, a LOH region is simply a region with minor allele copy number of zero. Whether it can be done on your data depends entirely on what copy number caller was run as they all have different output formats. ...
written 5 weeks ago by d-cameron2.2k
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Answer: A: WES or WGS
... The answer very much depends on the mechanism of action of your drug. If your drug is an ALK inhibitor, you absolutely need the ability to detect ALK fusions. WES is good at finding point mutations in coding sequence, but is terrible at finding fusion genes. In the case of ALK, you'd be looking at ...
written 6 weeks ago by d-cameron2.2k
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Answer: A: Structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumour types
... I've been using the calls from the PCAWG final public release: https://dcc.icgc.org/releases/PCAWG/consensus_sv https://dcc.icgc.org/releases/PCAWG/consensus_cnv At 2749 SV call sets and 2778 CNV call sets across ICGC and TCGA, that's more than the claimed 2,658 and means some samples are missing ...
written 6 weeks ago by d-cameron2.2k
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Answer: A: How to Update/Edit INFO field of VCF
... You won't find a tool that works on your input as your input does not comply with the [UCSC BED file format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1), nor the [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format). At best, it's a [BED3 file](htt ...
written 6 weeks ago by d-cameron2.2k • updated 6 weeks ago by RamRS30k
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Answer: A: Is there a hybrid aligner that uses both long and short reads to align to a refe
... No such hybrid aligner exists since aligners perform read alignment independently for each fragment. That is: per read for long read, and per read pair for paired-end short read sequencing. A 'hybrid' approach would give the same results as aligning the short and long reads independently with the sa ...
written 8 weeks ago by d-cameron2.2k
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Are bwa alt contigs controlled purely by idxbase.alt?
... What is the source of bwa ALT alignment? The [documentation][1] indicates that: > bwa reads the ALT contig names from "idxbase.alt" Does this means that the index itself contains no information about ALT contigs? Would I be able to JIT assign a different set of ALT contigs for different samples ...
bwa written 8 weeks ago by d-cameron2.2k
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Answer: A: diffrent between CNV and pcr duplicate
... PCR duplicates are a result of a DNA fragment that was used to prepare the library has been sequenced multiple times. CNVs are changes in the actual number of copies of a section of DNA in the cells being sequenced. These are fundamentally different concepts. CNVs are identifed based on the aggre ...
written 10 weeks ago by d-cameron2.2k
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Comment: C: HPV EBV typing from cancer genome data
... Yes, kraken2 classifies according to where in the taxonomic tree it can place the reads. If that's just HPV, then it'll classify it with that taxId, if the sequence is unique enough that it can be classified as HPV 18, the it'll allocate as that taxId ...
written 11 weeks ago by d-cameron2.2k

Latest awards to d-cameron

Scholar 8 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 5 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Popular Question 16 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
Scholar 18 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 20 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 20 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 22 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Supporter 22 months ago, voted at least 25 times.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.4 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.5 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.5 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.5 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.5 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.5 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

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