User: d-cameron

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d-cameron2.3k
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Australia
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Posts by d-cameron

<prev • 267 results • page 1 of 27 • next >
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Answer: A: Soft Clipped read 3' end position
... > Is there a function like this to get the 3' read end positions excluding soft clipped bases? record.getAlignmentEnd() > How can I get the hard clipped 3' end of the read position where there is soft clip at either end of the read? I ended up writing a SAMRecordUtil class for SAMRecord o ...
written 9 weeks ago by d-cameron2.3k
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Answer: A: bwa aln writing speed became very slow after being very fast. What is the patter
... > using bwa aln bwa aln is designed for very short (<=50bp) reads with `bwa mem` preferable for longer reads. Why `bwa aln`? > However, after writing the first 23 GB at a fast speed, it only write exactly 1 MB (1048576 bytes) every ten or twenty minutes, though CPU usage is still near 310 ...
written 3 months ago by d-cameron2.3k
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Answer: A: Tools to call Large indels/structural variations in whole genome BAM data of mo
... Two recent SV benchmarking papers are: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1720-5 and https://www.nature.com/articles/s41467-019-11146-4 GRIDSS and manta are currently the best performing short read breakpoint callers, not sure about what the best-in-class CNV cal ...
written 3 months ago by d-cameron2.3k
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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 4 months ago by d-cameron2.3k
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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 months ago by d-cameron2.3k
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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 months ago by d-cameron2.3k
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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 5 months ago by d-cameron2.3k
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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 5 months ago by d-cameron2.3k
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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 5 months ago by d-cameron2.3k • updated 5 months ago by Ram32k
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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 6 months ago by d-cameron2.3k

Latest awards to d-cameron

Scholar 9 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 10 weeks 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 6 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 9 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
Scholar 16 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Popular Question 20 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
Scholar 22 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.0 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Popular Question 2.0 years ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Supporter 2.2 years ago, voted at least 25 times.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.7 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.8 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.8 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

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