User: d-cameron
d-cameron • 2.2k
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Posts by d-cameron
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1
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142
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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-cameron • 2.2k
0
votes
1
answer
159
views
1
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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-cameron • 2.2k
1
vote
1
answer
139
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1
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... 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-cameron • 2.2k
0
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2
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171
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2
answers
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-cameron • 2.2k
2
votes
1
answer
86
views
1
answers
... 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-cameron • 2.2k
0
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1
answer
189
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1
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... 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 ...
2
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1
answer
295
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1
answers
... 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-cameron • 2.2k
0
votes
0
answers
98
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answers
... 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 ...
written 8 weeks ago by
d-cameron • 2.2k
1
vote
1
answer
172
views
1
answers
...
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-cameron • 2.2k
0
votes
1
answer
145
views
1
answers
... 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-cameron • 2.2k
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8 weeks ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
5 months ago,
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For A: bwa and bowtie2 bamfile format
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8 months ago,
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For A: bwa and bowtie2 bamfile format
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12 months ago,
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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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16 months ago,
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For C: Deciding on a Variant Caller
Popular Question
16 months ago,
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For What are the sematics of containing bwa split read alignments?
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For A: bwa and bowtie2 bamfile format
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For A: Modernising the FASTQ Format
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For A: Modernising the FASTQ Format
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For A: Please, please, define what a 'read' is.
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2.3 years ago,
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For A: Please, please, define what a 'read' is.
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For A: bwa and bowtie2 bamfile format
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For A: Please, please, define what a 'read' is.
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For A: bwa and bowtie2 bamfile format
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